The place to start is with a good HU. The choices are endless. I'd decide you want mp3 playback capability and go from there. Pick a deck with the features you want and room for expansion (aux inputs and at least 2 sets of pre-amp outs).
Next, think about subs/amp. Do you want a 4 (or more) channel amp that can eventually run your entire system with or a 2ch/mono amp that will be used for subs only? How many and how big of subs? What type of enclosure? Box in the trunk, 8s in the rear deck, or something more custom?
Then, think about some replacements for the speakers up front. You could build some custom components that will sound teriffic for less than $100. What about amplification? Did you buy a multi-channel amp, will you buy an additional amp, or will you just run off the HU (not my personal choice but sufficient for many)?
Then, you've sound-proofing, maybe some rear fill type of speakers, etc...
The possibilities are endless with a grand.
BTW, I've never been a big fan of RF. You can get better equipment for less money.
