it is a trial and error thing, modding :)
I keep my older mod files by renaming them, currently I'm using v15 of my mod. If I screw up, I can use the Gibbed.Dunia.ArchiveViewer to view an older version and extract files (that worked) from it and then replace the new files (that didn't w%&k) with my old ones.
The patch basically is an archive of different files, some of which we mod, others that we don't touch (because we can't make any sense of them regarding usability in a mod). So extracting files from the older modded patches to be able to mod them again is efficient :-D
I had no luck with the Reputation Levels. I'm stuck with Rep2 but going to enter "world2" (Bowa) now which may pop the collected Rep ^-^ I'm almost hoping for that miracle, like, going to Bowa and *ding* have Rep.5 right away :-D
Well, Bowa reset my rep to 1 and the barge mission put it back to 2. The next buddy mission claimed to have increased my reputation but it didn't change the rep level which is still 2. By the way, when I said I'd need much higher values I actually changed them for all missions to 100. Now I doubt that it has any influence at all, just like the autoreload and trying to mod myopia into mercs. Hmmm.
Anyway, I had some time today but I reckon I won't be doing much soon, other things on my agenda use up quite some time.