There are other who probably know a lot more than I do but:
JSGME (if you're using it to load mods) won't read the differences between individual files. It simply loads the files in the order you specify. Meaning that whichever menu.txt is loaded last will be used by the game. To get all the changes for each mod in the same menu.txt you'd have to copy and paste the specific text lines into the proper .txt file and then make sure no mod is overwriting the corrected .txt file.
Clear as mud?
As far as looking at .dat files, I use SH3ditor. A brilliant little program that lets you fiddle with all types of files.
Hope that helped.
T
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