UPDATE:
So if you just use the RR.dat file (this contains the foward torpedoroom and aft torpedo rooms) and do not use the CR.dat, but use FM original file you will have both working together. Installing this way, I now have the open coning tower (provided you are using the modified FM file) and also some other nice things that come with Aces mods (urfishes fire effects, FM light maps, etc)
also crew manning the bow planes will leave their station when on surface as should be
but heres the issue-while you can see the new compartments, you cannot walk into them with out getting a "camera out of sectors" error.
So perhaps someone can modify the camera to go into these new areas?