Use a voltmeter or tester and check if you have power to the side marker plugs ofthe harness. If it shows you're getting voltage, the light socket may not be making contact to the bulb. I've run into a number of side marker sockets, both Challenger and Cuda, that look like they should work but don't.
If you don't have 12v at the side marker harness plugs, use the ohmmeter setting of the meter and see if the little metal bullet end of the plug is connected to body ground. (the "hole" in the harness plug carries the voltage; the bullet end is connected to the black wire ground).
For the taillights, run a little jumper wire from the light housing to a good ground and see if anything improves. Like Mike said, paint might be getting in the way of a good ground. On our Cuda, the rear turn signal lights are screwy without that jumper wire.
Anyway, you'll eventually get it. It's always a nice challenge to get all the lights working when you're bringing a car back to life. If the car is in the Bay Area now, I could probably help you figure it out sometime, but I'm guessing you'll figure it out.
