I have a new construction shovelhead with a stock Harley inner primary, Rev-tech 5 speed, BDL belt drive (enclosed), and High torque starter. The jack shaft is to short meaning the bendix gear comes off the spiral gear as it enters the ring gear on the clutch basket. The shaft is a later model, (7"). I can remove the inner primary and machine the mounting boss where the starter bolts up as there is plenty of material there to remove. I need to have the shaft to come about 1/4" out to work properly. Any suggestions? Thanks!!

 

I had a similar issue with my 68 FLH {if I understand what your problem is}
I installed an after market outer primary the bearing and boss for the starter shaft in the outer primary was different than the oem primary it allowed the starter drive to go to far out and as you it came out of the spiral gear. not good I didn't discover the problem until I was riding the bike for the first time after installing the new primary. I heard the starter running away down there after the bike started.
fortunately nothing was destroyed. after I got the parts all back together which of course involved taking the starter off and well you know...
I found another nut spacer which engages into the outer primary that was longer to take up the difference. I did have to have the new spacer machined to fit with the correct tolerance. hope you follow what I am trying to describe.
I would sure try and avoid any machining to your primary..

 

I'd need pictures of your setup to see what all you have going on in there , like since it's a 5 sp which inner you using the old 4sp style and starter or the later 5 with all the offset's and the later starter & shafts , ect . Photobucket is your buddy here .