Sorry, I'm no help with coupler height. The milled aluminum frame may or may not be a different thickness at the coupler. I always measure and adjust when necessary.
The deck should ride at the same height above the rail head so long as the P&D acetyl bolsters are mounted to the top of the frame and there isn't too much weight on the frame. The only differences in ride height I've experienced with P&D trucks was caused by different axle bearing spring rates. Some trucks I have from ~2001 F-unit kits use very soft springs that bottomed-out when I initially over-weighted the locomotive. Other kits I purchased years later came with stiffer springs.
As for picking up the engine by the shell, the tab arrangement may be stronger than you expect, at least until the deck at the tabs become worn. RC's 3-R models are considerably heavier than the 2-R. They have a steel chassis and a U-shaped steel weight under each drive shaft. Bill McClung told me that they are easy to convert from 3-R to 2-R.
All the best.
Bob S
