If ya could post a coupla pics of yer bike it would help, is it like the yeller un in the attached pic?
If so and the engine fits well (carb clearance comes to mind) then I don't think there'll be a problem. The shiftkit takes over your (unsuspended) crank sprockets so there isn't any slack caused by travel, the shiftkit itself is angled down quite a bit so I think you'll clear the shock & pivot easily. It's remotely possible that under full compression your rear tire might
come close to the shiftkit's jackshaft... I really doubt it tho and that's something you could fix with spacers/shims/standoffs for the rear engine/shiftkit mount anyway.
SBP has a pic of one with a slightly different rear suspension on their homepage: http://www.sickbikeparts.com/Images/FS-SBP.jpg
Great bike for motorizing BTW, gonna be an ossum ride