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I notice that JSGME throws up a warning that several files to be amended are already amended by other mods. Is this a problem?
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Obviously it is! Some mods only tweak one file. If that file gets overwritten by another mod, you will only get the last one you installed. Other mods use various files, and if some are overwritten, the whole mod might not work as intended.
My suggestion is to stay away from overwriting mods. However, if you learn a bit about what has been modified (And both RFB and FTT have extensive readmes about that) you might be able to combine some parts of them together.