Cujo, This thread went dead and I hope you got your printer working.
I have had every possible mechanical failure with my SD3.
My most recent failure has been the slipping extruder. Just like yours, the servo was clicking, not the gear stripping the filament, which I have also dealt with.
I used this site for the 100's of hours of troubleshooting. The multiple replies on this thread lead me to suspect a partial clog. After 5 full dis-assembly and cleanings of the HotEnd, it appeared that doing more cleanings while expecting different results would be futile.
I jumped on the PID cal, Servo Chip tuning, Hotter Temp, Hot Servo, Spring Tension, Buy an E3D, and buy a new Hotend red herrings trying to fix this clicking with no success.
During troubleshooting, in the home position, the extruder clicked occasionally. When I bumped the speed to 200mm/min it clicked worse but only after 2-3 seconds and 50 mm/min gave no clicking at all. The HotEnd temp was set to 210.
So, I tried printing at a much slower speed. There was still serious clicking on the first few layers so I suspected nozzle back pressure would make it appear like a partial clog. So I removed my 1/4" sheet of glass and air printed. It still clicked.
I took the advice from wardjr and ordered the E3D. Except I still needed to get the printer working in order to print the MK5.
So buying an E3D is not a solution to a problem, it is an upgrade to a working printer. Unless, of course, you printed a MK5 prior to the machine heading south.
As I could not waste any more time on this machine, I was going to give up like many others have done with their Solidoodles.
But then I replaced the Green Folgers filament with a spool of black that I had ordered from SD when I bought the machine and it has not skipped a beat since.
Obviously, the melting point of this Folger filament is much higher than the SD brand. I did not feel comfortable running the PEEK above 210 but will attempt to melt the Folger when I have upgraded to the E3D. It also seems like the viscosity of this filament is thicker than the SD filament even when thoroughly melted. It may not be all about the temp.
Also, curling of the extruded plastic happened with the Folger and not the SD. Even though curling would seem to be an indicator of a partial clog, it caused me to waste alot of time cleaning a perfectly good nozzle.
One final thing is that I had made some good prints with this Folger Green when I first started using it. Otherwise I woud have suspected it right off the bat. Folger may have different consistencies in their pellet batch. Don't know, but:
Bottom line, DON'T USE FOLGER and be very suspicious about cheap filament.