if you were going to add aftermarket radio components then truth be told you would have had to remove most of the factory parts anyways. So basically, although the previous owner had no clue what they were doing, you're not starting off in a bad spot.
ill try to keep this as short as possible and make this into basic steps in which avenue i think would be suit your needs. Just an opinion, not saying this is your only option
1. find the HU you want and buy it.
2. search on google for a radio wiring schematic for your car so you'll know the basic wires you'll need like the hot, ground, power intenna etc.
3. pick what wattage amp you'dl ike to use. (me personally i find subwoofers to often be overbearing and annoying after a while. I've always gone with a sturdy 4 channel amplifer and matched my speakers to the power output of the amp for the best over all sound)
4. pick you're speakers wisely! surf the speaker stores online and really read what their power output is both low, "rms" and max. you want to match that rms as closely as you can with the amp without going over. I.E if the amp reads 4 channels at 100 watts rms total power thats 25 watts rms per speaker, youw ant in the area of 20-25 watts rms speakers (make sense?)
5. don't look at the wiring nightmare. Run the wires to ur amp then to your speakers individually. take your time, this will actually make servicing the system easier than the original equipment down the road say if you'd like to upgrade or something.
6. enjoy it not only a sweet custom system you came up with but enjoy knowing you were able to do something yourself that a shop would charge you a kings ransom to do.