Another update:
1500 km now. Using the whole rev range on occasion and the motor has continued to loosen up and feels quite strong now. Also, I am not getting any false neutrals at all anymore. Not sure if the gearbox broke itself in, or if it just educated me as to what it wants from the rider.
Touring seat is an improvement but I'd still need a break if I rode for more than about 2 h I think.
Sintered brake pads made a big difference! I am also trying to train myself to use the rear brake regularly, something that was not previously part of my "style".
I am really adapting to the wide bars and feel a lot more confident in the subtle feedback they are giving me. I just needed to get used to it, it's so different from a sportbike. The Pirellis still do weird shit, especially the rear when accelerating hard out of a slow corner, but it doesn't phase me anymore because I know to expect it.
I am in the habit of going for early morning rides before work, to avoid riding in the heat of the day. It is so relaxing - with the upright riding position, flexible motor, and reliable gearbox, the bike just asks so little of the rider.
I am taking it really easy on the mods, since I like the bike so much as it is. I will probably mess around with lighter rear springs, once I can find the time to do some proper sag measurements, etc.