First of all, you don't need to spend 3 Grand for a tight system, you probably won't even need to spend 1500.
1) I would suggest going with an install that hides the amp and so on. You can buy top of the line speakers and still have it look stock, my brothers truck came with factory JBL speakers.
2)There are modifications that can be made to the stock h/u, but I would suggest going with a new h/u, more features, and better output. Believe me, a new h/u will look much better than a stock h/u. An 8" sub will give you good crisp sound, it won't get bone crushing loud, but it will give you nice sound quality.
3)This one is easy, tell the installer what you want, if he/she tries to tell you what you want, then he/she is not the one you want. Basically, you know what you want, don't let them talk you into more money for something you particularly don't care for. Honesty also plays a big factor, talk to them, get an estimate, then ask around about it.