When talking high quality systems that includes a sub and amp, a $1000 budget is a little small even given the fact that you have the deck.
But if that is the absolute maximum I'd suggest this (which is one we have done many times too just quietly)
Boston FS-60 6" splits at the front (doors and kicks)
Audison SRx4 amplifier
Jl 12W0 subwoofer
Stinger cable.
You would probably end up spending $1200-$1400 when you factor things like installation and sound deadening in but I tell ya what, the end result would be well worth it.