Yep.. Most of the systems will have reset.
The windows are easy, just run them all the way up and down a couple of times to reset. It's a standard thing on every car I've had with one-shot windows.
The gearbox will learn your style again (256+ shift pattern types apparently).
Not sure what the smaller wires do.
And the near-stall sounds a bit worrying, maybe just needs a wee blast about to clear things up
