The radio probably says "CODE" in the display, or not? If it does, you need to enter the security code, you should have a radio manual with the car to help you through this, and a gray plastic card with the 5 (?) digit security code, you'll need that to do it.
The windows probably just need to be synchronized, do they move at all? Look in the regular owners manual to do this. I don't believe the top will start to work until the windows are all the way down.
Worst case scenario is that the RST control module (under the false floor in the right storage well behind the passengers seat) may need to be disconnected and plugged back in (all 3 connectors).
The car was just jump-started with another car, right? These gas-powered jump start units that are on some tow trucks can really fry control modules.
Let us know how you're doing.