Sounds like you know what you're doing aligning the pilot with the sensor etc. We had a previous TT that I had problems with the water heater each spring it seemed. My solution each time was in cleaning the electrical blade contacts. I'd pull the blades out and scrape them with my knife and then reinsert. I believe the contact for the sensor was the one in question, but honestly it's been a few years and I think I probably just cleaned all of them I could find in the heater area. It took me a couple years of fighting the same issue before I figured out I just needed to clean them each spring, never had a problem after that.
Good luck.