Thanks for your replies. The problem seems to shift itself. At first it wasn't extruding fast enough. I don't know how to change the extrude speed in the firmware or slic3r. When I gave manual commands to retract it did get up to speed. I suspected that the reason is that it can't build enough presure to push it through for some reason. I tightened the springs on my airtripper extruder which only had the motor skipping steps as a result. I then tried to turn the pot switch screw. This didn't resolve the problem either.
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