"Could this have been caused by a military accident/incident? "
Yes, it might have been shot down accidentally. Or deliberately after what happened on 9/11.
"Could technology have advanced where it is possible to scramble/jam comms from a distance (maybe a ship) It kind of fits with some of the bizarre facts both official/unofficial."
Maybe but you'd need a big jammer that would be hard to hide.
"If comms/radar were jammed that could account for the plane disappearing from secondry radar. Wouldn't the pilot have headed back to land with a lower altitude to try and get bearings from the land mass which could account for the plane position when it was being tracked by primary radar."
No, not really. A fast moving aircraft - 500mph - would have to be jammed by another fast moving aircraft. It's not possible to have a blanket jamming like this would required. The aircraft would soon be outside of the area being jammed.
The radar (ADS-B) is not used for guidance or navigation. The aircraft would use two separate, independent systems. One is VOR - VHF Omindirectional Ranging which uses ground based transmitters to triangulate the position of the aircraft; the other is GPS. To block the GPS signal, you'd likely have to be above the target aircraft. You can't really navigate an aircraft of this size at speed visually at night. You have to do it on instruments. At night, pilots shouldn't even be looking outside - that has caused accidents through spacial disorientation as well.