I had a root canal that is now infected. I now have a thrombus on the interna l jugular vein. Ultra sound was done but, doctors are unsure?

Endodontic expertise. See an endodontist for the tooth problem. Often times they can fix the problem if the root canal was originally done by a general dentist i believe the conditions are not related so see an md also for the vascular problem!
Lemierre's. There is a condition known as lemierre's disease in which a retrotonsillar abscess can extend into the bloodstream and produce thrombotic lesions of the jugular veins along with other significant problems. I cannot tell whether this is true in your case, but woudl see an ENT doctor and get diagnosed. There may be other issues.