Attached are my cura settings for Ninjaflex for reference. Like an idiot, I modified two things and now my print looks awesome; so I don't know what fixed it.
First, I mechanically leveled my bed (added shims underneath). I was out close to .040" and now I have it within .005" in most areas, .010" at the worst.
Secondly, I did what you suggested. I did a load material through Mattercontrol. I said I was loading Nylon X even though it was Ninjaflex so I had the nozzle up to 260 and I just let it ooze out until Mattercontrol turned it off.
So, I'll give credit to both. I'm assuming leveling helped and who knows, maybe I had some Nylon X plugging up the nozzle a little bit
Once my print is finished, I'll start playing with speeds to see if I can go any faster.
I won't consider this issue resolved or closed but in the monitoring stage.