Those temps are fine. Pretty much all that heat is from the CPU doing something intensive and does not indicate a hardware issue.
Usually when you have a thunderbolt issue it holds down several main power rails making the machine unusable.... So I don't think you have a thunderbolt issue... OSX driver issue? Maybe.
I would back up your stuff and reinstall the operating system. The system has several sensors and will shut off if it gets too hot. 78*C is well within safe limits.