I'm not too sure about the electrical differences between mkiv years.. but I just know how meticulous most of the 20th ae guys are (you should check out the for sale forum at www.vwvortex.com).
Chances are, if there were an electrical issue, it would have been sorted out by now with new parts. I wouldn't let that train of though deter you from buying a car. they're 10 years old now, and these problems will have been sorted.
I just think that, for your budget, if you're looking at a mkiv gti, the extra factor you get with the special edition gti's (not to mention that 90% of them are enthusiast owned, babied, and nicely modded) is worth it over a regular gti.
I'd check out the vortex forums (are you northeastern?), and local craigslist and kijiji etc. there will definitely be something available, especially since the weather is getting nicer.