The "hood" above the center wire (electrode) and the "fork" at the top of the assembly are the flame-sense portion. Yours is extremely dirty. Use a "Scotch Brite" type scrubber to try to get it back to shiny. You can use a dollar bill on the electrode. Clean the mounting surface as well. Interesting that you were able to remove the pilot tube, they are usually very stuck.

Along with the high-voltage spark a very small electrical current is sent along that blue wire as well. When the pilot lights the flame (which can carry current) completes the circuit sending the current to "ground" and telling the system to open the main gas valve and stay on. That much dirt can cause enough resistance, especially as the metal heats up, that the control "thinks" the flame has gone out and shuts the system down to start a new cycle.
Cleaned up. I will try to install.
 

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The "hood" above the center wire (electrode) and the "fork" at the top of the assembly are the flame-sense portion. Yours is extremely dirty. Use a "Scotch Brite" type scrubber to try to get it back to shiny. You can use a dollar bill on the electrode. Clean the mounting surface as well. Interesting that you were able to remove the pilot tube, they are usually very stuck.

Along with the high-voltage spark a very small electrical current is sent along that blue wire as well. When the pilot lights the flame (which can carry current) completes the circuit sending the current to "ground" and telling the system to open the main gas valve and stay on. That much dirt can cause enough resistance, especially as the metal heats up, that the control "thinks" the flame has gone out and shuts the system down to start a new cycle.
OK. Good news is that it worked and no more cycling. Hot tub is heating up quickly. Thank you!

Bad news is that there is definitely intermittent drips of water, more on the right side near the plumbing, that are causing the flames to go orange and sizzle on that side.. The burner on the side is also showing more rust.

Sounds like I’m not out of the woods. I will try to inspect heat exchanger more closely to see if I can identify why it is dripping. Let me know thoughts.
 
Side question. Does the hot tub heat up faster with the bubbler turned off?

Does not matter. The heater puts a fixed amount of BTUs into the water. The bubbler probably causes some loss of heat from the bubbles as you are trying to heat it.
 
Once I get a closer look at my heat exchanger, I will post where the drops of water are coming from and try to take pictures. It is interesting because there will be no drops for a couple minutes, then there might be one 20 seconds apart. It is random.

At least, and the meantime, I can get some use out of my hot tub. thanks again for the help.
 
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