[cadillac512]

Gary, this is stuff that takes years to learn, and in my case, a lot of good information and research by folks who were nice enough to publish their work so we can benefit from it. It's interesting for sure!
If you have the brand and part number of the pistons you are using I'd be very interested in knowing. The situation you are dealing with,pistons "out of the hole" a bit, is pretty darned rare in the Ford flathead rebuild world unless the pistons are specially made like Bored and Stroked has referenced. It's actually a nice thing to have since you can get the clearance you want all the way to the piston edges. With pistons down in the hole, you are stuck with whatever you have on the outer edges. Can't mill a head to fix that!

I think you'll be delighted with the way this engine will run. Your work quality so far is way above the average home builder's.