Like TonyD said. When tuning only change one thing at a time. Some of those lists you showed are main, air, pump, and pilot in one step! Wow you Will never tune doing that.
When I switched from Webers to Mikunis I talked to Todd W. Sent him my engine, cam specs etc because my engine was more than the guy I got them from.
I have a 2.9L, p+p E31 .510/300 cam and about 10.8 compression.
39mm choke
155 main
190air
60piot
50 pump middle hole
35 degrees total adv.
Now haven't got to the dyno yet but I put in a wideband rather than just seat test and plug reading so far 14-15 idle, 13-13.5 light cruise and 11-12 WOT right to 7000. No stumble, no bog runs real nice. I also run Todd's stacks, short SK manifold and I'm at 1650 feet alt. Most of the 3.0L or bigger motors I've seen dyno sheets on with your cam specs run 39 or 41 chokes you might want to examine that.