i have a similar "issue".
I've had my stock 01 jetta alh since 2005. it's now 2014 and i finally have enough disposable income to throw some money at it. I just installed (this month) pp764's, intercooler, 17/22, tdtuning race stage 4 tune, buzzken 2.5 no cat no muffler, racepipe.
and it smokes, also smells a bit funky. the sound at idle is like a buzzing noise.
EVERYTHING about my car is completely different than it used to be.
but once you get used to it...... it's awesome!
you too, will get used to the nuances of smoke, odor, power, etc.
enjoy!