For softer filaments (TPU,TPE) I suggest the following setup.

Suspend your filament above the printer and "gravity feed".
Use a .50 nozzle.
Print at about 600 mm/min.

Generally speaking, you should get great results as long as everything is in good working order.

To test your harness try the following: Heat your hotend to print temperature. While watching your temperature plot, move the extruder assembly back and forth by hand. You are looking for large temperature fluctuations. If that happens, then the harness is the most likely culprit for your MINTEMP er...

Your description of the issue is consistent with your extruder harness having developed a fault in the thermistor wire.
Please contact us at support@makergear.com.

I would suggest contacting us at support@makergear.com.
We can help you trouble shoot what is going on.
A thermistor should never read 0°C. Shoot us an email
and we would be happy to assist you.

If you still get a MINTEMP error after replacing the thermistor on your hotend, then it is probably your extruder harness.
Do you have a V4 hotend? If so, you may want to upgrade to the metal motor mount.

Sorry to see that you are having this issue.
Please contact us at support@makergear.com
We would be happy to assist you.

I would be interested is seeing what is happening.
Can you send some pictures to support@makergear.com?

If you run that print dry (no filament) does the sound continue?
I would also check to see if the extruder assembly seems loose at all.

Please contact us at support@makergear.com. We would be happy to assist you with your z motor!

Did you download the M3 profiles for Simplify3D from the M3 Knowledge base?
https://makergear.zendesk.com/hc/en-us