The bore distortion is also lessened by doing an overbore, from what I understand, because of the many heat cycles that it's already gone through. None the less, I still put on a T-Bob 2 on my new top end build.
Yep, wiring harness rub through.. there was a recall for that, but if you pop the tank off, you can see the rub points, fix it up yourself with a liberal application of tape and tucking in wires. and know it was done right.
Deep Hole syndrome is not a big deal if you take care of it. I think I put a little allen head set screw with a dab of grease to hold in in place for assembly in the side case when I did the Doo.
Deteriorating rubber... ya, I think they were packed in a shipping container to the US that was filled with rubber eating gas. well nuts on the wind screen and the rubber on the wire to the starter rotted on mine. The turn signal stalks seem to be another issue, but mine are still original.
Yes both Cary Aspy and Eagle Mike have said that the bore tends to "stabilize" over time/heat cycles.....which is why the 685 works as a "fix" despite using the same sleeve. As you say, despite this, I'd still use a T bob to protect your investment. ....and yes, the other issues are relatively minor but probably still good for a new potential owner to be aware of.