I agree with Ross on the head unit, every Sony I've run or installed for someone had pretty anemic reception. Pioneer packs in a bunch of features for the money & their quality is top notch. PLUS if you wanna stiock with a stock sized head unit Pioneer makes several in the DIN & a half style (another choice is the Monsoon head unit from a late model F-body, see them on E-bay pretty often.)
As for speakers, for a "budget" system utilizing the stock mounting locations here is what I would recommend:
Rockford Fostgate 3 1/2" in the dash, (not sure what the model # is) recently checked these out at Best Buy & they sounded VERY good in the display room and even better in a Monte SS out in the install area.
Cerwin Vega Stealth Series 5 1/4" for the doors, nice crisp response, great quality for the price & no problems about being too deep.
For a component set I like either CV or Rockford Fosgate. Mount the woofer in the stock location & create a spot on the door panel for the tweeter (I will take a pic with a couple of spots marked out on an actual TR doorpanel & post it tomorrow) One thing to keep in mind here though is that we are working with a limited mounting depth on these cars, so quite a few of the high end (big magnet or built in crossover) 5 1/4" speakers available won't fit.
Cerwin Vega Stealth Series 6x9"s in the rear deck, nice fit & very good sound quality ESP considering the cost. Unless you mount a set of kick panel pods up front I don't recommend totally ditching the rear "fill" speakers. Just my opinion here but the stock door speaker location is not condusive to a ultra-quality front stage; the rear deck speakers will help offset this "problem." One alternative is to install a set of 5 1/4"s back there, which will allow the bass from the subs up into the cab more efficiently than just firing into the back of the seat, but doesn't totally junk the rear mid frequency "fill."
One thing to think about, a pair of 12" subs can be a bit tricky to mount on the rear shelf and still have the correct airpsace for your particular speaker. I would suggest a single 12" sub OR a pair of 10"s; again just my personal preference here. I run a single 10" which provides plenty of low end grunt for my musical taste, (blues, modern & classic rock) AND it isn't a huge weight addition so my track timeslips don't suffer too much from there being a couple of hundred extra pounds of MDF & stereo electronics in the trunk.
Doug C.