Yes, you can't just install mods, that JSGME reports as having a conflict, especially with cfg files, these have to be
manually edited and appear in only of the mods!

With these you have to combine the mods.
For example, I have a mod folder called "New Ships", and each time I add a new ship I disable the mod, add the new files & edit the EnglishNames.cfg file (within the mod), then I enable the mod again!

This way I can keep adding ships forever with no problems & when I disable it SHIII still runs without these ships with no problems!