Thanks for the Kitpack plug, but just be aware that it's not a perfect example: Some of the kits are a bit buggy. But the theory's good, so I guess it's safe to learn from.
1. There's no limit (as far as I know) to the amount of stuff that can be crammed into one SPL file. The only reason to break it up would be if different classes/kits would be using closely related effects, e.g., Kit A is immune to Sleep, Kit B is immune to Charm, and Kit C is immune to Sleep and Charm. Note: Make sure to use the "Permanent after death" timing mode for stuff like this. The plain "Permanent" mode is for things that wear off when you die, like Polymorph and Feeblemind.
2. DLTCEP has them listed (of course, otherwise you wouldn't be able to use them) with their full descriptions, but if you want to view all of them at once, they're also on IESDP. IESDP isn't a program, it's a website you can save to your computer, full of modder-helpful data. (Caveat: I've found some of the information, namely the kit abilities, to be somewhat inaccurate, but maybe I was working with an out-of-date version that has since been corrected. Besides, it taught me to always double-check everything with DLTCEP.) I'm almost positive you can find a download link for IESDP on this site, and their forum is at Gibberlings Three.
3. The numbering scheme is ABILITY1 through ABILITY99 . . . I don't know if you can put letters in there, or go beyond 99, but I doubt it, and I also doubt you'd need to apply more than 99 separate SPL files at any given level.
Everyone, including me, swears by DLTCEP for making spells. It's pretty good at items & creatures and stuff too, but for getting down to the real nitty-gritty you'll be using Near Infinity. Infinity Explorer is almost a must-have as well, but it's read-only, good for checking files & viewing animations. I also use DLTCEP for making the BAM files for custom icons.