With GWX, run the Museum and go through the various nations - which it will take a while... if you CTD in the Museum with GWX, then you have found a problem ship. It seems to me though, that if you haven't added anything to GWX, there won't be a crash there, but it has been a while since I ran the Museum there. It does take quite a while to load... Don't forget that you should be running the mod with the 4Gig Patch enabled.
Easier to do might be to download TDW's
SH Validator, loading the SH3 mode and run that. Also of use, though a little more difficult to use is Hebe Vollmaus's
mySH3-Tool, but once you get the cfg file set correctly, it will find things wrong that you never knew existed in the game... seriously. Both good tools for trouble-shooting - especially for the modders!