Does it look like this?

The water heater is a Bradford White. Guessing pilot flame is burning a little dirty causing thermocoupler to tarnish but don't know what to try. Heater is located in corner of garage and raised 2 foot off the ground. Could there be an issue with the vent coming off the top and to the outside of the roof? Thinking trouble must be in intake of air or gas from control valve.

Thanks for responding. So you think I should just disconnect the thermocouple? I thought that might be an option, but I figured I might as well leave them in there as a safety precaution, even if they're not that necessary. Does this make sense? Do you have any insight into the wiring? thanks again

As long as the cable fits into the clamp on the plug/receptacle body, there's no problem with just cutting off unneeded conductors as long as they are isolated enough to preclude accidental contact with a live terminal.