My 2001 Tiburon has the same problems your car has. My Check Engine light has been on now for approximately two years. It went off for two days after I had a new alternator installed but then the light came on again. My exhaust system is fine so the only thing left to do is try new plugs and cables. I've recently bought new spark plugs and spark plug cables so hopefully this will resolve the Check Engine light problem once I install them. I'll let you know. I will be using NGK spark plugs, not the Champion plugs that the manufacturer used (Champions are the cheapest plugs on the market).
The passenger-side power window still occasionally will not work for 15 or 20 minutes, but it eventually will start working again, usually within 20 minutes. Try using the passenger-side window button if the driver's-side button doesn't work. I looked into getting a new motor for the passenger-side window but estimates for this motor range from $300 - $500 and that doesn't include labor. But if your window will not work at all I don't see any other option than buying a new motor or trying to get a used one that still works from a junk yard.
