Very late update on my FID troubles-I have been busy with my GC since.

I replaced the jet and the H2/air flows looked more stable. I however ended up with other issues, as the FID output was very high (~500000), which made me think that something was shorting. After an unsuccessful attempt at replacing the spring (which looked bent), I ended up calling Agilent for help and all is now well after an engineer visit.

Learning every day!

Thanks to all for the help.