You have to read between the lines here. What these guys are really saying is "Welcome to func_msgboard, it's good to see a new face around these parts. We'll be happy to see if we can help you. And don't worry, there are no silly protocols here. If you make a mistake we won't hold it against you." Yeah, right.
Just some pointers to your questions as I am not well versed enough myself to give you complete answers:
1. And don't forget that any follow-up questions you have should go in the Mapping Forum
2. Unfortunately, it is not straightforward adding new/other monsters and sounds as they have to have their program code added to the progs.dat file. Check out the content of some of these links:-
These may give you a flavour of what you will need to get to know.
3. You will need to be able to compile your enhanced progs.dat: try Frikqcc (Google it)
4. I don't use Qoole but I would imagine that the monster data is held in an entity file somewhere in the Qoole directories. I am sure some of the visitors to this place can help further. I use BspEditor and there is a directory called Entity and the entity data file is called ents.qc - this is an extract:-
/*QUAKED monster_wizard (1 0 0) (-16 -16 -24) (16 16 40) Ambush
Scrag (Wizard), 80 health points.
the monster will only wake up on
really seeing the player, not another
monster getting angry
5. It would not be considered 'correct' just to add new items to the ID pak files, and if you intend releasing the mod for public use, you would be expected to keep all of your files separate from ID's. If you look at any of the publicly released mods you will see the format you need to follow. Try Marcher as a good example of a quality mod well packaged (OK, Kinn?)
6. And another thing that I don't know anything about is WinQuake. I think a lot of people now use modified engines and the one that seems to get most mentions around here is Fitzquake.
7. Try looking through the Mapping Help forum anyway. There is a tonne of information in there. Also look through Teaching Old progs.dat New Tricks on this board in the Discussion Threads area.
Mapping, mods, qc, monster ai etc, all good fun but it takes a lot of time and a lot of patience to become proficient. I have neither time nor patience hence I am not proficient.
Stick with it and you'll have years of enjoyment but beware of becoming too nerdish ;-)
Seriously though, if you post a question in Mapping Help, you will get answered. I've been coming here for years and asking all sorts of dumb, inane, pointless, obvious etc, etc questions and there is always someone who will come up with the answer. It's quite a happy place most of the time.