If you're only using those 2 mods you don't even need to merge those bundled xml files, from ghost mode description:
Compatibility with specific mods:
Preparations - do not merge effects_ep2.xml file. Make sure the one from Ghost Mode has a priority (should be like this by default as modGhostMode is loaded before modPreparations).
GM likely already includes the changes preparations makes to those files. Also in order to merge the differences between 2 mod's files KDiff3 needs to compare 3 files, A: the vanilla reference file, B: Mod 1's version of that file, C: Mod 2's version of that file.
Your script merger is only comparing 2 files because it can't find the vanilla reference file for that comparison, a bug fixed by the unofficial script merger patch.
Next time follow the install instructions first and post issues in the relevant mod's page.