You're going to get a variety of opinions on this topic, and i'll be glad to add mine. It sounds to me like you're looking for a more SQ-oriented setup that is capable of playing rather loudly. In my opinion a nice front stage, a good powerful amp, and a mid-level single subwoofer are likely to fit your needs nicely. As mentioned above some sound deadener is going to be important in that car to calm down all the little rattles and resonances as well. No matter how good the equipment sounds, if there is buzzing and rattling making you crazy you can't enjoy it.
I like to ask if there is even a rough budget in mind when I'm designing a system for my customers. Obviously it may change during the process, but even a rough idea can get you in the park. It's no help to spec a 3500$ system if you'd prefer to only spend 1500$, or the other way around. I always encourage most people to lay the majority of their budget to the amplifier first, front stage second, and then depending on the budget either the processor or the sub system next. There are great sounding systems for almost any budget, but obviously the quality leaps upward as you are willing to spend more on better parts.
Your analogy with the engines 90%/10% this is pretty right on. The thing about building a high end system that makes use of that last 10% is that you need everything in the system to be able to perform at the highest level(with one exception that I'll get to last). Buying the best subwoofer on the market wont do you any good if it's powered by a 99$ flea market amplifier, it will likely work much worse than a much cheaper woofer would. I sell a certain component set that I simply will not install unless it's being powered by a certain level of amplifier, because anything under level that simply doesn't work right and the customer wont end up happy. The exception is buying an amp that is of a much higher level than the rest of the system. You simply cannot buy "too good" of an amplifier. Even cheaper speakers will sound better with more, cleaner, better controlled power. And a high quality amplifier can provide you with great sound for dozens of years, while speakers by nature of their constant movement will eventually wear down. Again back to why I recommend people allow a large part of their budget to the amplifier. In your case you may even find a good quality 5 channel amp will serve you needs well, while saving a little space. The processor is a part that will help quite a bit, but only if you get the right one and use it correctly. I dont't bother with any sort of little 1/2 din EQ or the like most of the time. Most decent head units will do everything they can do, only better. You need something to truly affect the sound field with things like time correction. The BitOne, MS8 are 3sixty.3 are in my opinion the best options out there right at this moment. If they can be fit into the budget without having to downgrade the rest of the system they can make a huge difference.