If you want to stick with a GM3 I would use a screw drive and a shaft encoder. That is what HydraRaptor uses so I know it works reasonably well. In fact screw drive has a little more grip than pinch wheel when softer plastics are concerned. The main advantage of pinch wheel is speed but your McWire will not be able to keep up.
If you don't use a shaft encoder then you would need gears as on the version shown here: [
dev.www.reprap.org]. Otherwise you can't slow the extruder down enough without stalling for McWire speeds. With a shaft encoder you can go as slow as you want but I don't know if there is firmware support for it in the official release. I know Wade made a firmware that supported it on older electronics.
You could use a worm drive, I plan to use a Meccano one on a NEMA17 stepper, but it is only 40:1 so you would need a big wheel and a small worm. Worm drives are less mechanically efficient than spur gears due to friction but that should not be a problem as pinch wheel is a lot more efficient than screw drive.
For pinch wheel I think it would be easier to use the Kysan than doing your own gearing. I am not sure how slow you can run it. You may not need any further gearing. Perhaps somebody with a MakerBot can tell you how slow they can extrude before stalling.
Yes I think the final gear should be metal, although I have made a pinch wheel extruder with a stepper and tiny plastic gears. [
hydraraptor.blogspot.com] I have not run it long enough to know how it will last.
This stepper based pinch wheel extruder must be the easiest mechanical arrangement [
reprap.org] and will be more accurate than an open loop DC motor.
[
www.hydraraptor.blogspot.com]