You might try posting on the VW Vortex forum to get some feedback about the problem the vehicle is having...

http://forums.vwvortex.com/zeromain?id=1

Maybe post in "The Volkswagen Lounge," as the Emm-Kay-Eye-Vee forum is kind of a shithole (its like the Whoreslounge of that forum)

If you can find the user "Broke" he is the man when it comes to transmission problems.

As far as the check engine light... it pretty much comes with the territory on that generation of VW's, they have a lot of problems. I'd be more worried if one didn't have the check engine light on.