Quote: If it was square on all four corners, the exact same measureemnt on the top and bottom on both sides I would try the .090 If it wasn't square, especially if wider on the bottom than the top, I would have the intake cut on a angle so the bottom is tighter than the top by .0015 to .0030 I've had to have that done many times on lots of Mopar V8 You might want to put the intake on the motor and then use seveal intake bolts(not real tight, maybe 20 to 30 inch lbs) to hold the manifold in place so you can get aggressive on using the feeler gauges to get it measure the best you can before proceeding You can loosen them and try moving the intake to get it center also before deciding what measurements are where We don't calll these motors Hemiriods for nuthin, if it was easy all of them would be perfect Good luck
Yea, you are right, I can just imagine the poor guy that lays out the $$$$ for one of these and has to take it to a "shop" to diagnose and fix a problem like this. No wonder I am often the only HEMI at a 250+ car cruise in! So you are advising that I take a .030 cut from the top to .000 (where it is not sealing)to put more clamping force on the gasket? and use a .090 gasket? I am considering "Gorilla snot" sealer around the ports as well. No more "let the gasket do the work" for me! Just imagine what the vacume is at 3,000 rpm on the freeway with a 4,200lb. car when you close the throttle to exit! It reads 17" @ idle! It must be over 50" on deceleration!
If it wasn't square, especially if wider on the bottom than the top, I would have the intake cut on a angle so the bottom is tighter than the top by .0015 to .0030 
I've had to have that done many times on lots of Mopar V8 
You might want to put the intake on the motor and then use seveal intake bolts(not real tight, maybe 20 to 30 inch lbs) to hold the manifold in place so you can get aggressive on using the feeler gauges to get it measure the best you can before proceeding 
Good luck 