The .cfgs are the ship's descriptions, and the .tgas are the basic pictures. The others can make a difference, but you want to add the MFM last. You should be okay with that.
As to your second question, yes, the new mod will change things. I doubt the changes will ruin anything, but there is always that possibility. The good news is that if you don't like the result you can use JSGME to remove it again.
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