There are ways to tune a VRT that make the car run more or less seamlessly.
1. Jeff Atwood (C2 MS) makes great software for VRT's. His software makes VRT's run very smoothly. (ex: Herbehop, TekstepVR6)
2. HPA. If you have the money, you could pony up and buy the HPA kit. It too will run near perfect.
3. (my personal fave) Standalone Engine Management. Possibly the best option for taking complete control of your tuning. However, you MUST know what you're doing. But for the 12v VR6 you could run MS and be all set. Wouldn't set you back too much either.