Recent struggle with lack of extrusion during prints  

Recent struggle with lack of extrusion during prints

I assembled and used my mk3 without issue until about 2 weeks ago. So have perfect prints for about a month. I decided to update the firmware to 3.3.1 at the same time putting a olsson ruby nozel on. I adjusted my pinda probe and redid the calibration wizard. First layer calibration came out perfect. Now the issue comes when I go to actually print something. I use the default pla settings with no adjustments in the slicers. I use slic3r pe and prusa control and every print seems to either have a height issue or lack up extrusion issue. Sometimes it manages to not coil up the first couple layers and continues to print and the final product looks perfectly fine, except the bottom and possibly some thin layers, which makes me feel like its an issue with the first couple layers. I have double checked all the screws, played with the tension of the filament feeders, removed olsson ruby and put the factory nozzle back on. When heated up pla and filament feeder screws loose, pla flows perfectly through the nozzles. Is there some place else that can get a plastic jam between the nozzle and the feeder gears? I just heat the heat block piece in that area.

I am not starting to think if it is a pinda probe issue with height. During a live print, would the pinda prob prevent the tip from getting too close to the surface now matter what? So if it was too low, then the tip wouldn't be able to get low enough due to safety? I thought the first layer calibration would set this height and if the calibration came out good then it would reflect on the prints itself, but that doesn't seem to be the case. I am stumped now as I have tried everything except maybe this pinda distance I speak of and flashing to an older firmware.

Any help would be greatly appreciated.

Not sure why my images aren't loading in the preview but I included the links as well.
Here are some photos to help visualize my issue. If I can get a print to start it usually finishes, trouble is getting the first few layers to stay.

First Layer Calibration Results: https://drive.google.com/open?id=1p4euBJtPu9SsbtCFWX89aaMX-khZIYqr

First Layer of a print: https://drive.google.com/open?id=1I5GS9UETu243r_USy6omzg3hRtpiAR8k

Second Layer of print above: https://drive.google.com/open?id=1dx2NVM9eZ08HWF6ZSUuFyDRVF4x-uSjr

Bottom of a Print: https://drive.google.com/open?id=1JBPog9uWqWNqXLcMRQLtXCuKbUsbi64-

Completed Print from above: https://drive.google.com/open?id=1932OReItrLPDBXdCYaxYUARZnonY1v27

Bottom of another finished print: https://drive.google.com/open?id=179ebbk_0xGyxIugUvzEWbgfp0Z2d5p-f