Cruise Seems Lean

I'll assume your 55 mph comment is a legal disclaimer.
The fact that you could increase throttle (especially without going to an easier gear) suggests the jetting is not too lean.
Generally with a lean surge on the main jets, the only solution is to slow down. If thats what you meant, then yes try one size larger jets on each primary.

If its the other scenario (not jets) then it seems that its the overlap from idle/transition to mains that could use some fattening.
and/or possibly a hair less timing at that rpm.

Since there is a little hesitation from stop, maybe the first experiment is to slightly richen and possibly extend the idle/transition mix. For that I'd start with trying slightly more restricted idle air bleeds. See how that works, especially for the off idle hesitation.

Yes, 55mph was legal talk. Yes, at any speed it will accelerate very well. Stab the throttle and there is a stumble, which normally I would think of adding a larger squirter, but these center squirters are new to me. If I ease into it (or post split second stumble) it pulls very hard to 6000 rpm at which point I let out or shift, etc.

For the "slightly more restrictive air bleeds", is that where people are using the fine wire sizes to test? Anyone have pictures as to doing this? I haven't gotten this far into fine tuning. I never had this issue when running the 3.91s. More RPM at cruise but lower speed.