Hi BeauKim,
thanks a lot for the response!
Yes, I have experience re-driling/doing screw conversions, I was even changing reeds for a period: the drill bits were brand new, I de-burred the holes, and verified the reed plates for the fit in front on the comb - it was flush.
I haven't checked the flatness of the comb, I assumed that Brendan Power might know what he's doing!

The inner wind savers seem to be ok.
I definitely didn't check for reed plate flatness, but looking through the comb without the mouthpiece assembly on and shining a light from the back I couldn't see any gapping anywhere.
The sanding after assembly is something I hadn't even considered.
I see that chromatic harmonica customisation is much more complex on the macro level, the diatonic is difficult on a much more detailed level:
the instrument construction on the diatonic is disarmingly simple, and getting it airtight is a breeze (pun intended). But setting up the reeds for overblowing is a real skill.
The chromatic might need a less specific work on the reeds (embossing and gapping certainly) but not necessarily fine tuning the arcing of specific reeds. The real skill seems to be in the air tightness at the mouthpiece level. I have to learn a lot here!
Thanks again! I will be playing the instrument as it is now, which is pretty good, and when necessary I will take the mouthpiece off again and sand the front of the comb/reedplates. If I did it now the Micropore tape would get damaged and I would have to redo it, which was not that much fun!