If I was you, I'd get some cheap speakers Lighting audio speakers for the front and back for under 100.00.
With a stock infinity system, why would he downgrade to lightning speakers that can be had for uner 100 for 2 pairs?
Personally I would drop the 6x9's in the front and go with a set of 6.5" component speakers (a little modification with some MDF and you *should* be able to fit them in the stock location if that's your desire). Type-x are a good bang for the buck set, running around $220 online. Then if you really want rear fill pick up a pair of lower end MB quarts or some infinity kappas, both decent speakers that are failry cheap. Say around $100 for that (guess). For two sets of speakers find yourself a nice 4 channel amp. PowerAcoustik has some amps that are very good for the money, say another $100 there.
The next thing is to upgrade the HU. Look at some pioneer, or that alpine is a nice deck that people have reccomended. If you can get high voltage perouts, great, otherwise not a huge deal. Look to spend around $200ish on the HU.
That puts you a little over $600 without shipping, so say $700.
Now, that should sound great....but if you're looking to add a subwoofer as well you can probably still pull it off for under $1,000. Look into possibly an av12 (
http://www.aespeakers.com) or possibly a used atlas. Both are great performing subs on a budget. That'll run you a little under $200 shipped (less for an atlas), which leaves $100-$150 for an amp. Not sure of impedence matches because I am not looking at the subs right now, but a solid amp is the directed 750d someone mentioned they had for sale. You can pick up a refurb for $100 from ikesound (not sure how much the seller wanted here //content.invisioncic.com/y282845/emoticons/smile.gif.1ebc41e1811405b213edfc4622c41e27.gif) which is right in your price range. That amp does 600 watts at 1 ohm, 400 @ 2, and 275 @ 4 IIRC. Don't get fooled by less than 1000 watts though...in the right enclosure and efficient driver doesn't need anywhere near that much //content.invisioncic.com/y282845/emoticons/smile.gif.1ebc41e1811405b213edfc4622c41e27.gif
So over all, my reccomendation. Get a set of components for the front, rear fill speakers, an amp, and a new HU. Those should always be the first components of a system to be upgraded. After that, if you've got money, think about a sub and sub amp. I reccomended some stuff, but that is by no means the "best" or a comprehensive list of equipment, look around and ask some questions about certain things and decide which is best for you.