1.) Dished piston will not effect the quench distance, they are not dished all the way to the edge, only in the center.
2.) Yes, you got the right understanding, no you are in right field now !!!
http://www.probeindustries.com/Chevy_350_2_5cc_Flat_Top_FPS_Pistons_p/l2256f.htm
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I wonder where we differ, because I get a completely different SCR and DCR that you do. I looked up the Probe Piston and the only things that matched your info and picture were the Probe L2256F pistons with a 2.5 cc valve relief .... what are you using???
For engine 1 & 2, the only change was IVC angle of 64° and 66°. Engine #2 has two changes, gasket thickness.041" to .051" and IVC angle of 68°. I have to say, I really don't like a quench distance of.051" even thou the both CR decreased. I believe you gave up as much as you gained. If you never go over 5500 RPM, then you can do as 2old2fast suggested and go lower to .035" for you quench distance.
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I would verify my deck height with a straight edge and feeler gauges. Just make sure the straight edge is directly over the piston pin. You should be able to get close enough to verify what the machine was suppose to do. Besides not every block is the same.
BTW, what camshaft are you using and I mean give the part number or post the cam card with the specs
You can get the above calculator except for the Cranking Pressure at :
https://tbucketeers.com/threads/dynamic-static-compression-ratio-calculator.12683/