Jim, the CCC system will automatically adjust the carb for most any condition, so no need to consider changing jets, rods, etc. Headers per se should not cause a lean condition. If you had a radical cam with a lot of overlap, then it is possible to scavenge some of the fuel mixture from a cylinder that has not yet fired, but I don't think you have such a cam.
Most likely there is a small vacuum leak. Header bolts not tightened ( or re-tightened after a few heat cycles) can cause a lean condition. If you don't find loose header bolts, then I would also double check your TPS voltages. A TPS being off , or having a flat spot in it's resistance curve, can cause a lot of issues.
I've also had the check valves in the AIR system go bad, cause some funny running issues.