Quote:

I have a indy block 4.5 bore 4.375 stroke. My old setup had a 6.535 rod.

Was that with B1 valve reliefs or standard/Indy head valve reliefs?
As you have found, more stroke should have a longer rod, and that makes the piston shorter and puts the oil ring in the pin. But that is not a show stopper, just a compromise if that is what you must do. The B1 valve reliefs require the top ring farther down, so the ring pack gets tight/lower.