Hello everyone, and thank you for the suggestions. Today I used a 10-32 NF die to clean up the threads and it worked wonderfully. The only difficult part is getting the die started straight and true in the existing threads then gently treading it back and forth along the threaded area until it turns freely without resistance. Transfer line nut now threads on with ease.

I know what you mean about the transient air and water peaks when the PFTBA valve is first opened, it just takes some time to equilibrate. After my dead time run everything is back down to 1% or less. I don't really try to chance anything down unless there is an obvious air leak causing high pressure in the quad chamber or if the air signal (N2 m/z=28) gets above 2-5%