Beat me to it lol. Installing the middle pistons is a waste of time since block deck surfaces typically aren't wavy.
I made the mistake of only checking the height of one piston back when I put together a 360 LA with KB107s and Magnum heads. You likely have one deck taller than the other, hopefully not by as much as your quick and dirty measurements show because .040" difference is quite a bit. Square decking based off the crankshaft centerline is the way to fix all of that but not all machine shops have that capability and it's more costly. Confirming how much difference there is between the two sides then having the taller deck milled down to match will still be a big benefit.