The simplest way for me to respond is probably going to be a one-at-a-time method.
1. Sadly, the 30-point allotment is hard-coded. You can get around it with the Recommended button as you've discovered, though.
2. You can remove skills, and the game will recognize far more than the vanilla eight, but the GUI will only recognize eight skills because that's all the game's .exe was programmed for. So you could revise the skills.2da to remove the unused/combined skills' rows and just use your own.
Unfortunately, you could potentially run into issues where a script isn't possible to de-compile and you happen to need to change a skill check in that script to get around this.
3. In a round-about way, you could do so. The game has four "hidden" inventory slots that are not represented in the GUI. These slots are the CARMOUR, CWEAPON_L, CWEAPON_R, and CWEAPON_B slots in nwscript (I presume these to be "Creature hide slot", "Creature left weapon", "Creature right weapon", and "Creature bite weapon").
You can use scripting in the start of the tutorial level (in the script that adds equipment by level, for instance) to add the required item to the player's inventory and equip it via scripting, since the player can't access the slots in-game.
4. Your guess is correct in how you'd go about doing that. I can probably get a good tutorial going throughout the week and have it up either during the week or the next weekend on all the tools and where to start.
5. The skill focus feats are in the files, but I don't know if the game's .exe was coded to recognize them. Sadly, we cannot actually control what the "passive" feats (any feat that you can't physically use) do or make our own, as the effects of "passive" feats are hardcoded into the .exe.
6. Sadly, the only way to do this would be to boost the CON score, but that'd be for every level. There's no way to do this so that it only affects the first level at character generation.
7. Unfortunately, the attribute progression is hardcoded into the .exe as well.
8. New classes are definitely possible, though I believe we've always had trouble with doing the spellcaster classes and the game crashing.
9. There is a way to limit which spells are available to which class, which would allow a psuedo-Talent system, but for it to actually work, you'd need to keep the three-class system Bioware implemented. So it'd be a toss-up between "Jedi character progression" and "Specialized access to powers".