Looking for advice on a blueprint engine.

That’s a great idea. I have been reading that the longer rod increases dwell at tdc, thus allowing a little more compression. Uses shorter pistons which reduces rocking in the bore. But puts the wrist in closer to the oil rings. Weird deal is the 396 stroker is a stock bore on a 350 block

I am sure there is some hot rod math out there which tells the story.
you are wrong on the piston length !
shorter pistons will rock faster than longer ones , think about it ...