Keep the amplifer, use it to power your speakers.
Keep the head unit.
Throw away the subwoofer.
hold onto the speakers for now.
Spend all your money on 2 subs, an amplifier, and a wiring kit.
Aim for a system with 2 ten inch subs, and around 1000watts rms amplifier, then you will need wiring for all of this, get an amplifier kit with at least 4 gauge power wire.
The reason I am aiming for this for a setup, is because you want 2 subs, I think 2 10s will be good for the limited air space you have in your vehicle, also this will save money, and require less power.
Less power requirements mean you hopefully will not need a new battery, new alternator (very expensive), will also help with budget.
Now you want most of your budget going toward your amplifier, a good chunk going towards the subs, and a smaller ammount for the wiring kit.
say 350 for amp, 200 for subs, and 50-60 for wiring kit
Looking at your budget for a setup like this I would recomend these things:
subwoofers:alpine/infinity/ssa/Dayton audio/TC Sounds.
Amplifiers:audiopipe/sound quebed/precision power/mb quart.