So I was unable to get it to come up again, I believe it was an instruction in my startup script for S3D. I issue a generic M109 Sxxx in the script to wait for the nozzle before a prime line, but it was early enough the 2nd extruder wasn't selected, so it was attempting it to the un-used 1st extruder? Specifying now 'T1' followed by the M109 next line.
Either way I also forgot I did indeed get the 300 celsius thermistor, that may have had something to do with the PWM adjustment to get rid of the warning. As soon as I changed the extruder max to 300 it went away. Same with the bed from 110 preset max to 120.
Everything is working great now though 🙂