Under extrusion, jamming, and first layer issues (I think they are related...)  

Under extrusion, jamming, and first layer issues (I think they are related...)

I have a mk3 upgraded to a mk3s.  It is a bit of a long story, but I had some issues with the thermister and the heater block, and decided to replace the entire hot end.  Since I have done that, I have had some issues that I think are caused by under extrusion.  Often on successful prints I will hear the extruder skipping steps.  When loading filament, the string coming out is a lot thinner that it used to be and kind of curls to itself as it comes out of the nozzle.  I am currently having an issue where there is an incosistent first layer, and then the printer jams for a good part of it, before potentially working through the jam.  I have tried different fillaments, and why the results vary, there is always some form of the problem regardless of the filament I use.  I have attempted cold pulls, but they came out pretty clean (it is a fresh hot end after all).  Does anyone have any suggestions?  I am not sure what to do to fix this at this point in time. The linked image shows an example of the first layer on my most recent print. https://drive.google.com/file/d/1LEaGJfIGkPr8hSlJuKpNG8Bj0uoTgi1s/view?usp=sharing