Right:
how do I make a point defense sytem that acctualy works?The current point defense system took more than a year to make.
And it works.
how do I make a better AI?AI is still rather difficult to make.
Even when it's possible, it's a rather fudgy area to just define "better".
There is however a visual tool included in the SDK, check the mission scripting tutorials on how to set it up.
And there is a person who really has a nack for this. But he made sort of boid (or flocking) system. One of the "simpler" types of AI.
how do I change the collision detection?Hard coded, we can't even change the force it relays (or make it "ignore").
We can however disable it (even for a particular object->object pair or object->type of object, no shields btw).
basically how do I change the more complicated stuff in BC(cloaking,shields,engine sounds,changing the warp system to a hyperspace jump on my mod only using some pics I have?...etc..The closest system to this is the one in DS9FX.
We are looking into making it a modular system, but this got snowed under due to an intern.

But currently it's fixed for wormhole travel.
You mean the tutorials above as the stickies?
Those are reposts. See the threads for the original credits.
These are also posted on BCU. In fact, these are reposts from there.
All the scripts you describe above are highly complex scripts (if I were to rate them, I would say double to tripple A level), not something a beginner would want to do without knowing BC deeply.
In fact, not even the advanced scripters here know everything there is to know about BC. And knowing my memory, I only know things when I run into them. It's not something I can just pull out of it and present it.
The Cloaking sound script is in fact a very easy script.
You may want to try and redo it yourself as practise.
And as Sovereign says, what would you like to change about the shields, etc, etc?