Rather than trying to write a treatise on the workings of the car, what I'm going to try to do here (and always tell me if I'm talking crap), is to discuss the basics, and how an understanding of them can suggest a plan for modifications. (If you've visited the site before, what I've done is pooled the stuff I had in the two modifications pages, and made it a bit better.)
Right, well the first thing to say is that Skylines Downunder have a nice section on modifications, so I'd suggest checking that out, as well as Graeme William's troubleshooting page. I'll try to add something useful, mostly piecing things together from magazines, and my chats with more knowledgeable friends. Now please bear with me if it sounds like I'm talking shite at any point; I may well be, but completely unawares, and at least I'm trying. 8) Just let me know (nicely!), and suggest corrections/improvements.
All I've done to my car at this point is to take off the mudguards (the car doesn't get particularly dirtier, and I reckon it just looks that little bit sleeker), and got rid of the horrid ding-dong box, the instructions for which you can find in Graeme William's troubleshooting page. It was imperative I did this, because the thing was so bloody inconsistent you never knew where you were, and if you relied on the 'bing bing bing' to keep your speed down you'd be in major strife. (And it was just bloody annoying anyway.) Sometimes it would go on at about 105 km/hr, sometimes 110. Sometimes not until about 120. Then again, sometimes it didn't go at all, and when you realise, and slow down from 120 or wherever you were, it sometimes started once you'd reduced your speed to about 110km/hr. So, all in all, a major piss-off. And it's gone now. 8)
As far as I can figure, the important things about a car's functioning to consider when planning what to do to it, are: Power, which can be further broken down into air and fuel getting in, the two igniting, and then exhaust getting out; Handling, including stopping; Monitoring what's going on inside the engine you've been pissing about with; and the Looks of the car.