In the middle of a 60 hour print (3.5 hrs into raft) and filament stops and restarts every couple of inches. Head continues, but extrusion cycles on and off. Extruder is not clogged and I'm on the 3rd layer of the raft so not too close to table. Filament extrusion just stops extruding for a spit second every couple of inches and then re-starts- almost feels like it retracts a bit if you hold the filament between your fingers. So I have missing filament every couple of inches on the part. I thought maybe this was just during the raft so I let it run over night. By the morning, I am well into support material and some part and the problem is still the same. Reset printer and tried same part again - same problem after about 3 hours. Is this something in the gcode? If so - what do I look for?
Well is it the actual retraction? Because the printer is supposed to do that occasionally. And if you have the retraction settings tuned incorrectly, then you could easily have it retract and then not enough filament comes out later on.
Why don't you post a picture and your factory file (file > save factory file)