Well, from the beginning: Had the cylinder in a vise to put the studs in, lightly of course, held by the cast flashing at the bottom. It slippped and broke a piece off. Now I'm pretty sure cast doesn't bend, but for some reason on the cylinder on the bottom I wasn't able to get the piston through. It was rubbing some down on the bottom and I could see where it was on the piston. I honed it some and that helped but it was still rubbing, so I started slowly grinding some material away down by the flashing where it was rubbing till the piston fit, then sanded smooth. It is below where the rings seal off, so it shouldn't affect anything besides piston-wall clearance IMO.
I'll check the squish tonight, does it matter which of the heads I use, will that change anything?