Another noob wanting opinions for a system.

[Reallunacy]

Ok, I'm new to the car audio scene though I've always been a fan. I'm wanting to get some opinions on what speakers/sub/amps to put in my 2002 Intrepid. I'm wanting to get a 600.4 amp for the speakers and 1000.1 for the sub/subs. My car is made for 2 6.5" speakers in the front doors and 2 6X9" on the back deck, but I have no problems learning a little bit of fabrication. For the subs, my goal is to remove the bench seat in the back and install 2 buckets and allow the subs to point into the car that way. I would prefer to not use my entire trunk but if needed I can. Clarity is a big deal to me and as far as price goes, under $2500. I plan on upgrading to 1/0 wire for future builds I may do and would like a suggestion on what amperage alt I should get. The wire, alt and deadener aren't included in my budget. Any advice is greatly appreciated.