Hi there,
The following pictures describe my issues well. I have tried several proposed solutions to no avail. This is the first time I have had a problem that is fixed by a little fiddling.
As you can see there are several point in each layer where little to no filament gets extruded. I have still been able to get some good prints but not without slowing the machine waaaay down to <30 mm a second.
This of course is a problem because when it's too bad, parts break off as seen in the final picture.

I have tried the following:
-A cold pull to clear nozzle.
-Switching filament types and brand.
-Slowing down machine (helps a little but not all the time)
-Tuning the E0 stepper driver for more current.
-Taking apart extruder assembly to make sure the gears were not slipping. (They weren't)
-Increased flow rate a small amount.

Possible relevant settings:
Print temp: 200 C
Slicer: Simplify 3D
Speed: 2400 mm/min
Layer Height: .25 mm
Extrusion Multiplier: .92
Nozzle Diameter: .4 mm

Any help is greatly appreciated.

Layer 1.jpg
Layer 2.jpg
Whole thing.jpg