Thanks for your feedback Bob.
The issues with Engine Mod are a bit mysterious: Both mods share exactly the same files, but the Engine Mod with it's default name loads in front of this mod, so this one would be completely inactive and should cause no issues.
Whatever caused this to be different in your case, once you have the Engine Mod running you will have the ground avoidance bug back as the Engine Mod source shares exactly the same typo in it's source code.
Regarding the spacing between aircraft on carriers I've heard about this several times already but didn't have time nor ressources to investigate.
I'm an FMB idiot so I don't have any mission to test and compare.
As much as I can see from code, there might have been issues with the transition from the stock's staggering to the catapult positions, but that's just reading from the sources, I would have to see and compare this with a mission capable of showing off all differences.
As much as the engine mod is concerned, this one is currently completely dismantled and being put together step by step. All the versions we've had so far were a complete mess code-wise (no complaint against their developers, just as a matter of fact the starting point was messed up already and so is the result). The outcome is currently uncertain. It might very well be that the whole Engine Mod thing will be abandoned once 4.13 is out, we'll have to wait and see.
Best regards - Mike