Extruder issues

I have been trying to get my Prusa i3 printing, but I am having difficulties with the extruder. While extruding it will at random moments start shaking/stuttering and stop turning. I thought it might have been a clogging issue, but the problem still occurs when the hot end is removed and the filament is just being pushed out the bottom and the filament can be easily pushed through the cold end by hand. The problem does not occur when there is no filament so I don't think it's the motor or gears at fault. Are there any obvious reasons this would be happening? Could it be that my hobbed bolt is covering too much of the hole for the filament?

I am new to this forum and the printing world. I just bought a pursa i3 kit and have it all assembled and all my axis home and work except for my extruder. I know my stepper motor works because I have unplugged my x axis control and used it on extruder and it worked just fine. I have heated the hot end and bed still no luck, i have even swapped out the pins for the x and e0 and even e0 and e1 still no luck.

I have the arduno mega 2560 with ramps 1.4, using marlin with pronterface as my control.

Can anyone please help?

whats the line up with the groove in the hobbed bolt.

also you _might_ have a slight mismatch in your extrusion speed compared to the software settings. It's a Open Loop design (no feedback system for autocalibration). Is it on any particular size print?
Also it _might_ be that your reel-to-extruder path has tension? What's the distance and braking you've got on the spool, and what kind of anti-tangle set-up have you got?

I've got a similar problem myself - but it happens about an hour into the print, so it's a bit of a bother to diagnose !

Can you upload a photo of your extruder? Printed geared extruders can have a binding issue if the print isn't clean up properly - there can be a lip on the bottom face of the gear that can cause binding. Cleaning it up with a small file helps.

If you have a printed geared extruder, you can check for binding by rotating the gears by hand. It should be easy to feel where / if they bind.

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