welcometo the site,
but i wouldn't swap your car, keep it as a daily and get another car for a project.
vr6 jettas are so freaking cheap now compared to 5 years ago when I was into vw's, all the time and moneyin a swap ain't worth it, neither is having your car down for repairs.
you can find vr6 jettas from $1000 and up. I bought one this past fall for a winter beater, paid $1200 for it, was pretty clean but an auto, it was a 98 w/ 125k miles, loaded etc.
So yeah, spead like $1500-$2k on a clean mk3 vr6 jetta or gti and then turbo that thing, that'd be fun.
good luck.