Doing a conversion to a Freon alternative like R134A can be done. For R134A you must change the a/c system oil from mineral oil to PAG oil (R134A is incompatible with mineral oil). You might also want to change to a larger/more efficient reciever/dryer unit, although I don't think this is strictly necessary. You will need to attach the different fill/bleed valves (each different refrigerant type has a different thread for the fill/bleed ports to avoid accidently mixing).

To perform any of this work yourself, you must first get the system emptied of Freon at a licensed shop (they have the capture equipement required). Installing the new components is staightforward, but on the VR6 car getting at the various connectors (for things like the reciever/dryer and compressor) will be difficult/impossible without lifting the engine out. Once everything is back in place, you'll need to get the system evacuated (for a period of 30 minutes minimum) to completely dry out any moisture, then have it filled. This is best done at a professional shop, since the equipement to evacuate the system is expensive to own.

As an alternative to R134A, you might want to consider FRIG-C, R406A or some of the other alternatives now available. FRIG-C and R406A are direct drop in freon replacements and require no modifications to the exisiting systems. I've been using FRIG-C for 1 year now in my '84 GTi Rabbit...no trouble and great cooling. You can find out more about FRIG-C from the Pennzoil website (even has addresses of places that sell the stuff...). R406A info can also be found on the web.