Bryan, for emission reasons the USA FJ’s were factory jetted lean with the #37.5 pilot jets.
Those small jets seem to clog easily, especially on gravity flow FJ’s. Remember, you are dealing with a 35 year old tank without the benefit of a proper fuel filter.
Perhaps it’s time to spend $25 for some new #40 or #42.5 pilot jets?
The slightly larger openings seem to be more resistant to clogging.
http://rpmracingca.com/proddetail.asp?prod=Carb%3APilotjetI had a clog at the end of Sunday's ride. It was missing badly until 2500 when cold, and 2000 after it warmed up. Fortunately on my ride today it cleared up. If I ever go back into the carbs again I'll put the bigger pilot jets in.