You are right, and here is a better answer.
Generally shifting problems for pans and pan style boxes come in three categories:
2. clutches and hub; and
3. forks and dogs.
Linkage is the easiest to spot and fix. I will address these areas in no particular order. This is relatively easy stuff so don't think you can't do it right the first time.
CLUTCHES & HUB
Start with the clutch pack. Remove it with the washer trick---just take a larger washer (or two to cover the hole on the outer adjusting plate), remove the locknut on the adjustment screw, put the washer(s) over the hole, and screw in the adjustment screw and the locknut. (An old valve spring collar reversed works fine.) Now put a wrench on the locknut and a screwdrive in the slot in the adjustment screw. Tighten the nut but don't turn the screw. The end result should allow you to compress the 10 clutch pack springs as one unit with the outer most pressure plate and the adjustment plate acting as a sandwich with the springs held in place.
Now remove the 3 clutch plate adjustment nuts and pull off the clutch plate/springs as a single unit. Set the unit aside and leave it alone for now. Remove the clutches and the inner plates. Remove the clutch drum. I assume you already removed the primary chain.
To remove the clutch hub nut it helps to have the standard home-made clutch hub tool. This is just a single old clutch plate---one with the holes that the clutch hub fingers go through--- with a steel bar welded to it---maybe 18 or so inches long. You will use this tool to hold the clutch hub when you remove the clutch hub nut.
Look at the clutch hub nut and you should see a lockplate behind the nut. Actually you will see one or more of the lockplate locking tabs bent against the flats of the clutch hub nut. Shame on you if you don't have a lockplate. Take a screwdriver and bend the tabs flat against the clutch hub so you can remove the nut.
THE CLUTCH HUB NUT IS A LEFT HAND THREAD. Put your home-made tool on the clutch hub fingers and hold the clutch hub so it will not turn. The manual says to use your hub nut wrench and smack it with a hammer until is comes loose. That works fine and I don't like using impact wrenches when I don't have to. Mine normally come loose with just pressure and no hammer pounding.
That brings us to the next problem---how to get off a highly recalcitrant clutch hub. Here are the tips---DO NOT USE A CLUTCH HUB PULLER. All this can do is mushroom the threads on the mainshaft and ruin it. Remove the clutch rod that runs through the mainshaft. Screw the clutch hub nut down against the hub but do not tighten it. Back off the nut one full turn. Here come the trick to this:
get a socket that fits the clutch hub nut and put an extension on it. Put in on the clutch hub nut. Sit on your seat from the left side facing 90 degrees from the normal sitting position when you ride. You should now have the clutch hub down below your legs somewhere around ankle level. Take a 5 pound sledge hammer and raise it up about 12 - 18 inches from the end of your socket extension and let it fall by gravity squarely striking the end of the entension. You will have to strike the extension with the hammer in a rythmic succession 2 - 5 times to set up a harmonic on the mainshaft. When you get this right the clutch hub will walk itself off the end of the mainshaft and you will see it come loose. If the clutch hub has been off before it will easily come off. If it has never been off before you will have to strike it a little harder and maybe a few more time. I usually smack no more than 5 times then I stop for 5 or so seconds and then try again if I have a clutch hub that has not been previously removed. DO NOT GET CARRIED AWAY AND BEAT THE HELL OUT OF THE CLUTCH HUB, etc. This method has never failed me.
What to look for that causes shifting problems:
A. worn / grooved clutch hub fingers are a serious no-no. Replace them and for all practical purposes when they get that bad, replace the entire clutch hub.
B. bent clutch hub fingers. Replace them or replace the entire hub.
C. clutch drum bearings---either balls or rollers (or a worn out bearing cage) that are shot to hell or missing. You can squeak by using rollers and the right cage over a ball type that has grooves in the clutch hub bearing surface if you can't get a new clutch hub--- but then plan on redoing the job in a few thousand more miles.
D. steel friction plates that are grease soaked, rough, rusted, bent, discolored from excessive heat, or have the little shock absorbing ball bearings missing or that won't pop out when you depress them. The plain steel plates after you clean them should be straight, smooth, and shiny. If any of these problems appear get new steel plates.
E. grease soaked clutches. Every now and then some ten cent genius claims soaking greasy plates in gas or other solvent will reclaim them. I think not. This might remove the surface grease but the first time the clutches heat up more grease will rise to the surface. Get new clutches.
F. cracked or chipped clutches. Get new clutches.
G. elongated holes in your clutch fiber plates. Get new clutches and plates.
H. loose or missing clutch rivets. Rivet on new material or get new clutches and plates.
Incidentally, now that the clutch hub is off, remove the rear drive sprocket and take a look at the trans seal and the condition of your mainshaft. Some corrosion on the mainshaft where it is exposed to the elements is normal and means nothing. THE REAR DRIVE SPROCKET NUT IS ALSO LEFT HAND THREAD.
Try to move the mainshaft up and down by hand. Any movement is not good and you will need to disassemble the trans and replace either the mainshaft, the bushings or the large bearing behind the kicker cover. Actually, any movement will probably mean seriously worn gears as well. I will not in this message explain how to rebuild the entire gearbox.
Replace any bad clutch parts. When you reassemble the clutch, grease the hub bearing and put a SMALL dab of grease on each of the steel balls on the steel friction plates. I mean it-----a SMALL dab.
Somewhere along the line take a look at your ten clutch hub springs and let's hope you have the right ones. Pan type springs have a shorter length than mousetrap eliminator springs. Put in elminator springs and I will be surprised if the clutch works at all. I did that once and nothing worked.
NEXT---LIDS AND FORKS.
This, too, is pretty mindless all in all so don't be afraid of it. It helps if the trans is out of the bike but it is not the end or the world if it isn't. Just be more careful NOT TO DROP shit into the trans when the lid is removed---like the small fork cap rollers / steel donuts. If one or both of these is/are worn or missing you will have shifting problems.
You will need the shifting fork alignment tool. Maybe someone else knows how to get around using one and doing the job right but I do not.
First, put the trans in neutral. This is when both one fork is between 1st and 2d gears and the other fork is between 3d and 4th gears.
Look carefully at your forks. If they and the clutch dogs look OK, not discolored, no worn dogs, no bent forks, no grooved forks, etc., you may be OK. I normally remove the forks for a closer look. I suggest you do so as well.
Before I remove the forks I use the alignment tool on the lid and then check the forks with it. This will tell you where you might have specific problems.
To remove the forks remove the small screw that holds the fork shaft in place. Loosen the shifting lock nut tabs and then the nuts. Get some vice grips and clamp them on a free spot in the fork shaft. Tap the vice grips lightly with a hammer and slide the shaft out of the case. Remove the forks and remove the nuts and lock tabs. SAVE THE SHIMS / WASHERS. These come in .007 and .014 thcknesses. They don't wear out.
Take a look at your shifting clutches / dogs and the inside of their mating gears. Rounded clutch dogs and rounded gear slots probably means new clutch dogs and new gears.
To reassemble: Put the clutch forks, shims, lock tabs, and nuts back in place and slide in the fork shaft. Tighten the nuts. Using the alignment tool, take the small steel rod and mate the alignment tool and rod with your lid. Lock down the alignment tool slider. Remove the small rod and now do the same for the other side. Remove the small rod and transfer the now properly spaced alignment tool to the top of the gearbox. Look carefully at the position of each shifting fork. Get each fork centered between its own set of gears. Gears go across the box like this---1st is closest to the kicker. Second is next---third is next---and fourth is closest to the primary chain.
Here is the trick to setting forks. Read this until you understand it. Each set of gears, 1st and 2d, and then 3d and 4th, have a false neutral between them. If is possible to shift part way between the gears, like between 3d and 4th and when 1st and 2d are in true neutral, and catch a false neutral. This is called false neutral because true neutral is between 1st and 2d. When the trans is in neutral the forks are centered between their respective set of gears. When you shift into 1st, the 1st and 2d fork moves to the right away from 2d and engages the clutch dog moving the fork and the clutch dog into the recess in the mainshaft first gear. When it fully engages you are now in first gear. When you shift into neutral the fork moves back taking to clutch dog with it to a position between 1st and 2d gear---now not being engaged in either 1st or 2d gear. At the same time 3d and 4th are sitting in their own neutral position. When you shift into 2d gear the fork moves left taking the clutch dog with it in the recess of the mainshaft 2d gear. You are now in 2d gear. Notice that 3d and 4th are still sitting in their own neutral position. When you shift up or down between 3d and 4th the same thing happens to those gears but this time 1st and 2d are sitting in their neutral position. A BIG PROBLEM CAN HAPPEN WITH IMPROPERLY SPACED OR WORN FORKS WHEN YOU SHIFT FROM 2d TO 3d. As you shift from 2d to 3d the 1st/2d fork starts to come out of 2d and move back to its neutral position. At the same time the 3d/4th fork starts to move toward third gear. If the spacing or forks are bad then you can lock your trans into two gears at the same time. If you are lucky all you have is instant trans parts all over the road and you will live to tell about it.
To avoid this major bummer, all you have to do is equally space the shifting forks, then shim each fork one .007 shim AWAY FROM each other. I have done this for years without a problem. This will give you an extra .007 spacing when you shift out of 2d and into 3d and vice versa. 2d will shift out of 2d that much faster and 3d will shift into 3d that much slower after 2d is already disengaged, and vice versa. It is cheap insurance and it works. You will not notice slow shifting at all. Incidentally, you should already have all the shims you need on the fork shaft. Just rearrange them like I indicated.
My other trick is that I always replace the forks and fork cap rollers/donuts every time I check the forks..
Don't forget to bend the lock tabs.
Don't forget to replace the shifting fork shaft screw.
HOW TO ADJUST A CLUTCH PACK
Assemble the clutch hub and clutch pack. Don't forget the lock tabs on the sprocket and clutch hub nut. Incidentally, I like the later hub nuts because of the new style seal. With pan clutch springs, adjust the outer pressure plate until the inside of the outer plate is 31/32s " from the inner plate. With new clutches this is right to spec. With somewhat worn but still good clutches, you turn the lock/adjusting nuts each equally one click at a time until the clutch grabs. I once had to use old and crusty knuckle springs that I had to turn down to 3/4ths " before they grabbed. At that point they worked fine and lasted for years that way.
HOW TO ADJUST A CLUTCH ROD
Turn in the clutch rod adjusting crew until the shifting arm goes back as far as it will go. DO NOT TURN THE SCREW TIGHT WHEN IT STOPS. Then back off the screw about one full turn. Hold the clutch arm with one hand as you turn the screw with the other. Hold slight pressure against the arm toward the front of the bike to make sure you turned the crew until the arm is all the way back as far as it will easily go. Now hold the screw in place with a screwdriver and lock down the locknut. It use a box wrench for this and smack it medium light with a hammer to set it against the outer spring plate. When you kick out the clutch the clutch arm should strike the back of your lid and stop in that position. If your clutch plates are then not fully released (with the bike rolling to a stop), turn in the clutch adjusting plate screw about 1/2 a turn until the clutch releases.
NOW YOU PLAY WITH THE LINKAGE
Adjust your clutch cable if you have a foot shift and it you have a foot clutch, you may need to lengthen or shorten the foot clutch rod from the rocker pedal to the clutch arm. Shorten it up if your rocker pedal stops against a foot peg, bracket, etc.
Adjust your mousetrap into the nearest trash can, the sooner the better, and get an eliminator.
THE FIRST TIME YOU RIDE AFTER ADJUSTING THE CLUTCH
Be careful---you may have not adjusted it just right and you might have to tweak things somewhat. Feathering the clutch in 1st for 10 feet or so until you get a feel for how it grabs and MOST IMPORTANTLY HOW IT DISENGAGES is critical the first time you test it.
With a jockey shifter arm there is no adjustment. With a tank shift, you know that better than I do so have at it and good luck. With a jocket ratchet shifter there is no adjustment. If it won't shift you possibly have a mis-timed ratchet lid. Read the manual for that. For a ratchet foot shifter, the rod adjustment should be simple enough for you to figure out.
I hope this helps.
New Knuckleheads? Thank, you, Jesus!!