It's been a few years, but is there a wave plate in the pack you say stacks too high? What did your stack measure? Same number of frictions and steels???
On my 3-4 clutch pack, I have .054" clearance. The "guide" calls for .060"-.083". Is the .054" sufficient?
I have always tightened up the clearances a little on any of the trans' I've done (20ish) under the assumptions that 1) the shift would occur quicker 2) they will become larger with use. I'll ask my trans buddy what he says for these.