What type of precision measuring tools do you have access to?
The reason I'm asking is if you can get, beg, borrow, rent or steal, JUST Kidding on the theft, a decent dial bore gauge or a decent set of inside and outside micrometers so you can check the I.D. of all the main bearing bores with the mains caps and bolts torque down with the bolts and then recheck them after installing the studs to see if the studs affect the I.D. or out of round of those main caps
If they check good, less than .00025 differences, I would run it as long as you have at least .0027+ main bearing to crankshaft clearances
If your really going to add the turbo or super charger later or sooner, within the next year, leave the short block alone now as far as the compression ratio
On your deck height differences if you didn't use the same rod and piston in all four corners you may be seeing the difference in the rod lengths, not the deck height differences I've seen .008 difference in rod center to center lengths out of the same stock 1968 H.P. 440 and similar results with stock street hemi motors and 340 motors
With a true 7.5 to 1 compression ratio you can run regular pump swill with the blower up to 4.0 lbs. of boost and still make a hoop of power compared to the same motor N/A
As far as piston to head minimum clearances with the blower I would shoot for .045 to .055 cold to the closest part of the piston and heads, check all eight pistons at TDC and rock the piston so each side of the piston rotates as tall as it can get when changing directions on firing
I run E85 in my bracket car with 14.5+ to 1 compression ratio, it works very well in this application, better than race gas ever did
Get that boost mounted and working soon
Good luck on your deal