Hey Greemon! I gave the mod a shot and I'm really impressed, great job!
For the record, we have no problem with mods, we're all for people tweaking the game and some of these I would call definitive improvements, like the ruthless route ending counter.
We've put less emphasis on global affection in the latest builds (0.4 onwards) because it stops players from making choices that make sense to them, one thing I'd add to the mod is an option to toggle the guide on or off.
The only problem here would be futureproofing it, since we do make small alterations to old files (for example, using a filediff with the work in progress 0.6 version of the script_build05.rpy file shows we've fixed some typos, made changes to show Kota's new casual outfit in one scene, etc. and we plan on doing small rewrites such as rewriting Luke's hangout scenes).
By all means don't let us stop you, thank you for the contribution!