I've not really done anything to the pickups, but I did take a tiny little bit of material off the bracing the neck pickup sits on, and I shimmed up the bridge pickup (with mouse-pad foam) as high as it will go without interfering with the strings.
That probably mostly personal taste : I like a lead pickup that's a hair louder than the neck pickup, and the way these guitars come stock is the other way around.
I do plan to wax pot the underside of the pickup assemblies again (not the coil, doesn't need it) so they're a little bit of a tighter package. the magnets can get loose and rattle on these NS Franz pickups.
I haven't changed out the wiring harness yet because I'm
1) Lazy
2)admittedly, not really looking forward to it
3)I haven't really had to - it still works, even though the pots are scratchy, and there's more wire in the guitar than there needs to be - you can hear it rattling around in there sometimes. But on stage, I play the big archtops, and the M75 gets drop D duty for a few tunes, or it's the backup guitar in case I break a string. I do play it quite a bit at home, but there obviously the scratchy pots don't really bother me.
My experience with archtop harnesses has been that it's a good idea to use Gibson style wire with the braided shield around it, because that allows you to "build" a pretty stiff harness that sits how it's supposed to by itself - then it's just a matter of slowly and carefully loading it into the guitar. On a stiff harness like that, get one pot in place, and the others usually don't need much help.
when making the harness, I make a cardboard template with the pot locations like they are on the guitar, and I don't allow too much slack for wires going to jack and switch. I use a bit of twine to get the switch in the hole, and large medical style tweezers to manipulate the pot shafts or move the harness around in the guitar to where it's supposed to go.
I've gotten semi-handy with it, but I go very slow, and it'll never be a fun job I look forward to.