Agreed; definitely give MAK a call.
Based on what you posted, a few other things come to mind:
1) What was the ambient temperature, and how often were you opening the lid to check the pizza? Every time you open the lid you are dumping heat out. That can add a lot of time to your cook, especially if it's cold.
When we cook pizzas on our MAK we go about 375° for about 20 minutes. If we have two pizzas, one on the top rack and one on the bottom, we quickly swap them about half way through and add another minute or two to the cook time. Otherwise we leave the lid closed.
2) Bear Mt. pellets are alder-based. Try using one of the oak-based brands and see if they perform better for you (higher BTU rating).
3) On cleaning the thermocouple: The MAK thermocouples are stainless steel and pretty stout. We've cleaned ours (on three different MAK's) with either a damp soapy Scoth-Brite, or a small piece of damp S.O.S./Brillo pad, followed by a wipe down with a paper towel, with no problems. MAK actually says to use a Scotch-Brite or similar pad on the MAK thermocouple to keep it clean and shiny.