Before going into my issue in detail I want to mention that I am using a QU-BD extruder...I know, I know...
At any rate I have to roll with it right now because I have nothing else. I have however upgraded it to use Barts modifications shown here:
http://www.thingiverse.com/thing:38281/#files and I am also using a MakerBot extruder gear. When I do a small print things usually turn out OK however during longer prints I get an issue where the gear cuts into the filament and it stops extruding. I believe that the gear is just getting too hot and this helps it to cut into the filament. I am running the QU-BD heatsink and fan during a print (also tried without to better see whats going on). I know I could try throwing more fans at it but does anyone have any other ideas for helping to cool down the gear?