First off, congrats on the new car! A 93 with 90k miles is a good find these days. About the paint, it's possible it got repainted if the door jamb doesn't have a paint code sticker. On my car, the driver's door was replaced (and painted) before I bought it and the paint code sticker is gone.
Do yourself a favor and get a nicer CD player, don't bother repairing a stock one. The stock player is actually 4-channel, and the four speakers in front are run off the front 2 channels. It only has to be 1 DIN, so you can have the storage pocket underneath it. I use that for my wallet and my phone while I'm driving, so I don't have to carry them in my pockets.