My first Thermoquad tuning question!

Make sure the choke levers are staying in the right spot. If that moves the secondaries won't open, nevermind the air door.
Check the vacuum levels and the step up spring. If you're not at WOT the rod hanger is still being controlled by the spring and it might not be anything close to what you need. That's normally the issue I have the biggest problem with on Tquads - that step up spring and lack of replacements.