well the window regulators are a big big problem and a few years back there was a class action lawsuit against vw and the regulators. I would still replace both regulators to fix the window. another reason that the windows are acting funny is because of the ignition switch. this is also another very common problem that causes many wierd electrical problems. its a 7 dollar part and fixes many problems.

now for the CEL problem you should get it scanned and post the codes up on here so we start diagnosing from there. the jumpy idle when the ac is on is probably a combonation of a dirty MAF and throttle body. i really think you need to get on www.vwvortex.com and get on the mkIII forum and post your problem up there after you get your codes scanned. many many people will be willing to help you try to diagnose your problems