One of my pet peeves with Harley service manuals is that they will often describe how to do something with no explanation as to why it should be done in that particular way. If the "how to" happens to be counter-intuitive, it often leads to the method being rejected by the technician. Evo/ Twin Cam head gaskets are a good case in point.
The reason for the factory headbolt tightening sequence is to equalize clamping force instead of equalizing torque. A torque wrench is at its most accurate at around 14 to 16 foot pounds. At higher torques the readings will be more affected by the friction of the threads and washer surfaces. By first getting an even clamp load at 14 foot pounds, and then drawing the assembly together an equal distance on each fastener(controlled by the amount of the turn and the threads per inch), you will theoretically have a much more even clamp load than you would get by using a torque wrench for the whole procedure. The torquing pattern is based on "pinching" the oil drain passage first for the best possible seal there.
The only drawback to this method, is that even at the 14 ft lbs, some of the torque is being used to compress the head gasket, so in practice you will not get a perfectly even clamp load. The solution is to perform what is known as "torque cycling". To torque cycle, just tighten in the normal sequence (all of the steps), loosen all bolts (in the recommended sequence and in 1/4 turn steps to avoid distortion) and then repeat the normal tightening sequence.
One other thing to keep in mind. It takes considerably more torque to start a bolt moving than it does to turn it once it is moving, so always tighten your bolts in such a way that the torque wrench is still moving when it clicks. (ever torque a bolt where you come to the end of available swing without clicking, but after you ratchet back the wrench clicks immediately?) When you retorque a bolt, you are not really checking to see what the torque was on it, you are only checking to see if it takes more than what your wrench is set for to get it moving again.
One last thing, because the engine does "grow" so much as it heats up, keep in mind that when your engine is cold, it has the least amount of clamping force on the gaskets at that point. Always warm up your engine before putting a load on it.