Currently swamped, but I'll tell you what I ended up doing. I made a class variant of each class, and in that you can remove skills from Class Skills add what you want to be Class Skills. This is what I did, except I didn't collapse my skills, so I'm not sure how I'd go about that. I did exactly the same as chiefweasel suggested, I duplicated my d20 system and made changes to it without touching the main d20 files. I've got my skills doing exactly what I needed, which is three-tiered Class Skills (1 for 1, max HD +3), Cross-Class Skills (2 for 1, max [HD+3]/2), a General Skill (1 for 1, max [HD+3]/2). Those kind of a changes could have broke my d20 files with all the altering and testing I did, so a duplicate set of files is always a good way to start testing and trying out new ideas. With the exception of a few special cases (which I believe I will at some point find a solution to) I've got my system jumping through hoops.
