Paul,
Install it over GWX. As far as I know, it will not change any non-environmental portion of GWX. By no means am I an expert though.
Disable the GWX 16km atmosphere-MEP3 is a 20km mod. MEP2.1 is the 16km mod. Pick which one you want, but I would think you need to disable the GWX 16km no matter what. I had the unofficial GWX20km mod installed and I disabled it when installing MEP3 and have had no issues. I've always liked the 20km mod.
You may have to disable your moon mod first. MEP may overwrite it. You may be able to insatll that back over the MEP mod, but I'm not sure. I'm not familiar with that mod.
I'm not sure I like the moon in MEP yet, I may have to experiment a little with some other moons. There are a couple of moon mods out there.
I have a few of the same mods running as you do and I have not had any problems.
The diesel smoke is a seperate mod by Rubini(I think

).
You might scan through the appropriate thread for any possible issues and ask more detailed questions there or PM makman94 who released the mod.
By no means am I an expert on mods. I'm always afraid of mod soup causing problems too, but I've had some pretty good luck, so far.
I wanted to get some submerged shots. It looks really nice underwater as well.
I have a NVIDIA graphics card(a 6600 I think) so things may look slightly different, and maybe waaaay better, than what I'm getting.
Like I said before, the best thing to do is try it out. You can always disable it with JGSME.
Enjoy!