Motorcycle Repair: starter jack shaft binding, through bolt, professional mechanic

Question
QUESTION: Just replace the starter with a high torque Thunderfire starter on a 02 Titan Gecko (custom with Evo style S&S). When the through bolt for the jack shaft is tightened (primary side) the jackshaft binds (starter has a manual solenoid button). Loosening the bolt frees it back up. I also tried loosening the starter retaining bolts and moved the starter around - this did not free up the jackshaft so I assume shimming the starter would not help. I put the old starter back on (it was burnt up) and removed the solenoid cover so that I could manually accurate it. It also was binding, may have been part of the reason it went bad in the first place. I have a copy of the HD parts diagram and believe everything is properly assembled. I am a professional mechanic although I have limited HD experience. I have spent all day messing with this. HELP!

ANSWER: Check the bolt to make sure its straight. Also, check the race for the jackshaft to make sure it is not worn to much
Good luck and happy riding
Mike

---------- FOLLOW-UP ----------

QUESTION: The bearing is perfect, the whole assembly goes in and out very smoothly when I just bring it up snug, but when I tighten it the shaft binds. The bolt has a bit of a bow, but the original bolt for the original starter is straight. And it binds when I tighten it also. The new starter uses a longer bolt because it is made to fit the earlier 1/4-20 or the later #10 arrangement. Could it be that the coupler is not square on the end? Maybe the hole in the back of the primary is not located quite right - what if I grind a few thousandths off of the shoulder on the starter to let it float a little before I tighten the starter bolts? Thanks for the input.

ANSWER: The only thing i can think of is that the inner primary hole is not square with the starter shsft. That would cause binding.
Good luck and happy riding
Mike

---------- FOLLOW-UP ----------

QUESTION: So -
A. open up the hole in the primary.
B. Grind around the shoulder on the starter and enlarge mounting  holes.
C. replace inner primary case?

Answer
The only things that can cause binding with your jackshaft is the race that the jackshaft slides in or the inner primary hole that the jackshaft slides in is not square with the starter.
Even though, when you do it manually, it seems to slide if can still bind in the race when you hot the starter button.
I would start by honing the race a little and see if that doesnt help. If it still binds then I would think you need to replace the inner primary
Good luck and happy riding
Mike