Extruder Clicking  

Extruder Clicking

Have had a Mk3 for about a year now and have not any any major trouble. For the past few weeks I have been attempting to do a roughly 4 day print but have kept having issues with the extruder clicking and ultimately jamming. I have tried to troubleshoot with availablke resources but nothing I have tried has resulted in any success. The first print I had was going smoothly printing with a .4mm nozzle and prusa galaxy black until I ran out of filament after about a day and a half. I paused it for the two weeks it took for the new filament and when I was finally able to restart it but the new layers would not stick so the print failed, no big deal I thought I could just restart the print. However, this is when I began to be plagued with the issues of the nozzle clicking and eventually ceasing extrusion altogether. I am at my wits end and do not know what to do and would like help to be able to finish the print.
Things I have tried:
1. Cleaned out the nozzle by running filament through and then doing a cold pull per the instructions on your website. Result: will print fine for about two hours before the problem occurs again
2. Printed in different filament. Results: the printer printed fine with hatchbox true orange pla, but I would like my final model to be in galaxy black as it is the perfect color for what I am doing and this project was supposed to be a quick undertaking not needing prep and paint
3. Cleaned gears, checked alignment, made sure pin was centered and screw on the drive gear was tightened as well. Also, tried adjusting the tension screw outside the extruder. Results: printed fine for about 3 hours before clicking resumed (at this point the .4mm nozzle had to be at 230 degrees for any print to work)
4. At this point I had nearly exhausted the entire second roll of galaxy black I ordered directly from prusa, and they were currently out of stock so I ordered from a third party this time, this is the roll that was used in #5
5. Changed to a .6mm nozzle (and made necessary adjustments to gcode). Results: print was coming along perfectly for about 50 hours but now clicking has resumes, and any of the above remedies only work for about and hour or two before the extruder starts to click again.
My firmware is up to date and I have tried two different model of the same design and nothing has been able to complete without the clicking, I am at the point where I don't know what else I can try and I need to know if it is a filament issue or a printer issue or whatever it is and what I need to do next to fix it. Any help I can get would be much appreciated.