I submit that your brain is still working out the calibrations with your new style of aiming.
Previously, you had the elevation calibrated. But you then begin seeking windage accuracy as you began your new aiming process.
You state that your windage is now working well with the new aiming system. This is success! Perhaps your brain allowed this adjustment to take place first for whatever reason.
As time goes by and many more arrows are flung, your brain will hit upon the windage calibration quickly, and then (hopefully) begin more efficiently adjusting the elevation sight picture. Your new aiming system has two distinct components with both windage and elevation. Perhaps elevation is, by unknown default, the second of the two to develop to your satisfaction.
I aim in a similar manner to what you are describing, and sometimes it feels like the brain is spiraling about the sight window and calculating the micro-millimeters between windage and elevation ... kind of like seeking the imaginary crosshairs in the sight picture's "scope" of view ... and all this within but a moment's time at anchor. All the while your body's machinery is manipulating the bow into that picture for the perfect moment of loose.
Hang in there, and good luck.