What are the before/after runout specs? Why was the crank sent back to Hoban the second time? Did you deal with John? If Hoban worked the crank, twice, the crank is not the problem. Could be clutch hub bearing? I have read that there have been lubrication and premature wear issues with the SE compensator; are you running one?
I don't know what the specs were..... Because the Moron that did the first build gave John the wrong weight. Did you deal with John? All of my dealings were with John. Great guy to deal with. If Hoban worked the crank, twice, the crank is not the problem. Could be clutch hub bearing? Already installed a new clutch hub bearing with the build . I have read that there have been lubrication and premature wear issues with the SE compensator; are you running one? I do have a SE compensator and a original compensator. I've installed both and cant tell any difference
Not trying to beat a dead horse, but you do have plenty of clearance around the nose cone on the cam cover from the front head pipe. I had some trouble there with my F/C.
As stated above the clutch hub bearing should be looked at.
Checked the exhaust from one end to the other. No touching !
What motor mounts are you using? The new style mounts are real stiff and take some time to break in. The old style were much more forgiving though they didn't last as long and got mushy after a while. Do a search on them and you will find a lot of posts.
The motor mounts were purchased by the mechanic about 11 months ago when the rebuild took place. I would think their the new ones.
The vibration is coming from the engine. Sitting still, I can feel it turning the throttle . I can put my foot on the primary and feel it stronger yet its the same vibration. The guy that tuned the bike used a TTS master tune. He was just learning yet he made comment about Doc not setting the tune right and he knew how better. The kid is a self proclaimed genius. NOT ! The bike does have backfire when first started sometimes till it gets warm. The throttle response is also sluggish till it warms up. You turn the throttle to quick and it will backfire or pop. I don't know what kind of tune he did on the bike butr I wasn't impressed. Nothing else he did was worth a crap. Thus the reason we had to take it to another shop and break it down and rebuild it. Everything mentioned has been checked out. The vibration is severe enough it has to be in the engine im guessing. I'm thinking the new piston rods are heaver than stock and the crank can't compensate for the 10:0.1 compression and pistons and it causes it to vibrate like it is. Just my guess. Or the tune on each jug is off to the point it's making it run that bad. These are all just my guesses. I don't know.
I'd go the tune route. The tune sounds all messed up. You must be ready to off this bike.
Get her tuned is the cheapest way to go. After that should this not work plan b is in order.
I would get with D/H and ask for the work order on the crank and see how they balanced the crank. No fault of D/H if they got bad information from the builder.