My V-Twin frame had the same problem. The reason your motor has a 3/8" gap between the front frame mount and the front motor mount is because the rear motor mount on the seat post is off a few degrees from level. At any rate, the first time my frame went back to Conn. for adjustment, that rear mount was tweaked downwards so the motor would sit level. But when the frame came back, I still hadn't fit a Pan motor in the frame. I put a Pan bottom end into the frame, motor fit, but the bolts were real tight on three, and the fourth bolt wouldn't go through the motor and frame mount. Frame mount holes were off a little. The top motor mount slot on the frame wouldn't line up with the top motor mount on the Pan motor. The frame went back to Conn. for some more tweaking.
The frame came back. No cuts or welds were made to the frame, but the motor fit now and the top motor mount on the frame lined up okay.
I put the '56 heads on and the rear head would not sit on the rear cylinder before the head struck the back of the seat post. I used a piece of tapered wood, tried to shoe-horn the motor completely into the frame. No go.
The frame went back to Conn. a third time for some more tweaking. Got the frame back, this time some grind work was evident at the top of the seat post. Don told me they changed out the front gas tank mount to an updated one they were using on their rigid frames now. Looking pretty good.
The only good memories I had with that frame so far, was that everytime I hauled the frame out of my pick-up to bare load it onto the UPS weigh-in table, I'd always collect a small group of people. One group of women said,"Ohhh, I've watched that motorcycle show on TV (My Two Sons)....I didn't know motorcycles even had a frame

And then once, some other guys that started in about what they used to own, and how they'd like to own another one. It was that enthusiasm that kept me going.
I got the frame back and everything fit. Had at least 1/8" + between the back of the rear head and the seat post. Looking good. Then I put the transmission in and found that the 5th mount was too high and wouldn't let the transmission seat completely on the base plate along the entire right-side. You've seen what I had to do to remove the top laminate plate. So all this has taken 9 years to fix and write a book at the same time. I'll post the pix I sent to Corbin-Don. Who by the way is a stellar person and is backing me to this day if I ever get in trouble with the rest of my build. He built a complete Replica Pan out of V-Twin parts last year, but he had a complete machine shop there at CG. Maybe you can see your problems in mine Mike. I know that Fuzzy had a Knuckle frame like yours and he moved the top motor mount on the frame back, but his motor still sat at a forward tilt. That isn't right. You might wire Corbin-Gentry or V-Twin and politely ask for assistance. But I think you're in a jam with your frame.
I won't propagate people getting dead-ended and building partial machines. It's not a legacy I want to leave behind.
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1. Motor won't fit into V-Twin frame.
2. rear head won't seat. Hits seat post.
4. Rear head keeps back of motor from seating on rear mount.
5. The above photos were with an old smaller set of '48 heads with plumber/O-ring conversions. This other set of (Accurate Engineering re-manfactured) heads are '56 and slightly wider even.
7. Top motor mount wasn't lined up right because of the seat post early contact.
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8. After Don tweaked things and made it right. Motor now fits into frame.
9. The correct clearance between the rear head and the seat post. Shown here is the older smaller head.
Shown here is the '56 wider head. Both fit. Frame is OEM '58-64. I don't have a pix of the tweaked V-Twin frame with the motor in it yet. But the motor now fits, as do all 5 mounting bolts.
