Thermoquad low vacuum readings

Both.

When you tightened up the secondary door, it comes in later and slower. That will enrich the mix. The door also may not be fully opening. 2-1/2 turns from a dead handing door is the suggested starting point.

The carbs secondary door should open up as soon as possible or as quickly as the engine can handle it without issue.

OK, not sure what "dead handing" is... Anyway, I can likely go back closer where I was, as it worked pretty well. Once or twice it would stumble/bog for a second when I really snapped the throttle down while cruising. Originally I had tightened the spring until the door just came up to horizontal, then 1-1/2 turns.

I'm trying to figure out what does what... So I loosen the door till it bogs when I stomp it, then tighten just a bit?

Did you ever get a lean surge before you raised the rod tree??

No, don't believe so. I raised the tree thinking it might help the mid rpm part-throttle application lean symptom. I have jets on order, and and as Rob said earlier, that indicates that the primary jets are too small.