Some of those issues (though by no stretch "all") are from the TMO / RSRDC combination. The RSRDC does not use some of those vessels at all, and they are basically "dead-ends", if you will. Once you have RSRDC on top of TMO, you might also run out of memory to run the Museum, and would have to use something like
LAA or the
NTCore 4GB Patch, to open up more RAM for SH4's use. However, lurker never did attempt to have the Museum run correctly in RSRDC, and it still might not make it through for you. Another thing about the SH4 game, is that each of the Main Menu choices are a different "mode" of the game, and after running one, you have to exit the game, and then re-start it, for it to allow windows to re-set its memory buffers. So if you did a Single Mission, going into the Museum will oftentimes result in a crash. The same with going from a Career run to a Quick War Patrol, or any other area of the game. The Museum loads up every asset not listed in the Museum.cfg file, and can eat oodles of RAM on you, and will sometimes not load again when you attempt a 2nd run, without exiting and then re-starting the game also. This does compound the time needed to "test" things.
As for the cfg (and eqp & sns) files, you can ignore the Land and Ordnance folders, but you do have "410 Rockin Robbins EZ PLot V2.0", which alters the cfg files, on top of CapnScurvy's OTC, and the EZ Plot mod does overwrite both it and RSRDC. I do not remember if RR made a version of that compatible with RSRDC, but if you remove that mod, you should see the number of missing cfg files drop considerably... RSRDC also alters the cfg files, sometimes changing the names of files inside the individual Sea folders, and the naming convention used might also be contributing to the issue. I do not have an RSRDC close at hand to check that, and for the life of me, I cannot remember what all lurker did for his mod...
