Is your new transmission calibrated properly for your tire size and axle ratio? Did you change the drive/driven gears? If not, your odometer may be grossly off and messing up your calculations.
If the Quadrajet's air valve spring is properly set, the secondary system will not open until the throttle is well advanced. So you are looking for issues in the primary fuel system, in the speedometer/odometer calibration, and in the timing.
3 degrees initial advance seems a bit low. I would set it to 9 degrees. What is the calibration on your distributor? HEI or points or ?? What is the amount of ported vacuum available at cruise for the distributor? Perhaps your vacuum canister is looking for more or less vacuum signal than it is seeing at cruise.
Rob's third gear suggestion is excellent.
There are a lot of variables. After your next cruise, shut down the engine from idle and immediately look down into the manifold below the throttle blades and see if any fuel puddling is present. There should not be any fuel puddling. If so, the carb has issues.
Vikki 1969 Goldenrod Yellow / black 400 convertible numbers matching