Have just skimmed the thread, but here goes.

I've been using a 3X9 6503 Ultegra set up since new all original except I replaced the R shifter long ago about 12 years ago. I used it for over a decade and then transfered it to a cross bike I made into a "gravel" bike, and then gave that bike to a friend. I still ride it when I visit. I consider it an excellent system in terms of reliability and versitility.

I've never considered it essential, or even with the design intention of any 3X system to have noise free access to all of the sprockets with all three chain rings. Just not a practical goal or essential need. Does anyone really expect that?

I always was successful at adjusting the middle ring to work with all 9 sprockets, and the large and small ring to work well with 7 or even 8 of them. That's what the front shifter is for! But I also found the middle ring with 9 sprockets to be effectively a good 1X system for a large majority of any ride I was on.

Carefully adjust your front and rear shifting and keep the 3X9. Aside from the hub compatibility questions mentioned above, and the expense of replacing so many expensive parts to switch to a 1x or 2x system that meets your needs, the 3X9 is a great system and worth making work satisfactorily.

If you need lower gears than what you have, simply get a 9 speed MTB cassette with the low gear you need and get an old Deore XT 8 or 9 speed RD off of EBay - the 8 or 9 speed versions are fully compatible with 8, 9 or 10 speed road shifters (the 10 speed MTB RD is not). My 3X9 group looks weird to anyone who notices or cares (very few), but great range: 52/39/30 and 11-34. Flawless shifting within the common sense limits of a 3X system.