Thermocouple with a built in safety overtemp disc verses a standard universal T/C?
By-pass the limit switch and see if the pilot light stays on. We've replaced so many of these limits, I can't count them anymore.

A few tanks have had a service bulletin issued to replace the entire gas valve / burner assembly. We've down about 8 of these so far. The parts are free at least and have solved the issue 100% of the time.

Sometimes poor venting is the issue. Check the air intake underneath the bottom of the tank if the screen wasn't installed around the base of the tank.