Ed, two possibilities come to mind.

First make sure there's no air leak around the carb bases. Or around the clamping screws.

Second is a trick I learned from Johnny Brodbeck, lo these many years ago. Uneven head screw torque.

Mount the slower turning of the two engines on a stand, and while running at peak loosen one of the head screws, and tighten it to just a little more than snug. If you have a drop in rpm with the first, go to the opposite side and do that one. Work your way around to all of them, what Johnny pointed out was distortion of the cylinder from uneven tightening.

Since your engines were fine before tear down I think one or the other of these is your problem. Assuming you didn't get the pistons and sleeves mismatched.

A twin flies better, a real go-getter.

Bill