Andy, thank you so much for taking the time to help me out, as per your suggestions:
The printer I have built: http://folger-technologies-llc.myshopify.com/collections/frontpage/products/folger-tech-reprap-prusa-i3-clear-frame-full-3d-printer-kit-ramps-gt2
The motor is not stalling, I don’t think, more jumping / jittering if I feel or hold the filament just before it enters the head it kind jumps a bit forward and then jumps back, but not all the time and only when the filament is extruding, i.e. some will extrude and then a bit will stall. Initially I thought the motor shaft was bent, causing a bit of separation between the gear and the idler pulley, but I have inspected it by eye and it still appears to be concentric, possibly the best thing now is to use a DTI to check the concentricity of the shaft, I did try to send a move to the control to spin the motor but it will not move unless heated. So I need to figure out how to ignore the cold prevention part of the code. Otherwise swap the motor for one of the others.
After the initial jam the gear did have molten parts of PLA in between the teeth, but I have since cleared this out, unclogged the main M6 shaft, cleaned the PTFE tube, and cleaned the build up inside the nozzle. I also tried using the head without the PTFE tube but that didn’t work either.
I have always reset the beds Z depth to 0 in all four corners, after disassembling the head.
One thing I have noticed, and only after this event is that the motor is very hot, too hot to touch, but saying that the X axis motor gets very hot also, noticed that one before the event, and have monitored with an external probe.
The only thing I can conclude is either the motor shaft is no longer concentric, the nozzle was FUBARed and no matter how I cleaned it, it was a losing battle or the heat soak has been getting up the tube due to incorrect reassembly.
I am a bit stuck now waiting for parts, I have accidently pushed the drill (by hand) through the nozzle thinking it was still a bit burred (this was the brass) and now I have a 2mm nozzle not 0.4mm
And the PTFE tube has been cleared out so many times it has seen better days.
I have searched the net for assembly photos with no luck, so I might model the parts and assemble them in Inventor to try to see what I have done wrong.
Thanks again Andy, if you or anyone else has any more suggestions please please post up.
Happy New Year All
Neil