Here is a couple of things I have run against. First, the plastic alignment tool has some pretty loose tolarences. I usually just snug the pressure plate bolts enought to hold the disk, but loose enough to allow disk to slide. I'll install transmission then tighten the pressure plate bolts by rotating the engine.
Second, I have run into a crank that was drilled for a 4 speed and had a bushing installed, but it wasn't deep enough. It was about a 1/4" to shallow.