Update: Both issues with my bike have been repaired, and both were fully or mostly covered under warranty. I'm picking the bike up this weekend. Per my dealer:
1. Tank was replaced under warranty with a new tank that has a slightly different design, which has spacers to hold it in place. Dealer said "I bet I know what the problem was, you didn't put the spacers back in" and I replied "no, the stock tank on this 2010 didn't have spacers -- that was a design change that happened after my bike was produced" (as discussed earlier on this thread). As usual, the people on this forum got it right.
2. Dealer fixed the problem with my 4th gear not holding. A clip was knocked out of place (possibly during the earlier repair) so the gear was slipping or sagging out of position. Dealer reports that in downshifting from 5th to 4th, sometimes the gear overshoots to 3rd, but I told him that was normal -- the transmission on my bike is just kind of loose.
Bottom line: these bikes aren't built to Honda quality standards, but that's part of their charm. They have personality.
To be honest, if i had it to do over again, I might have bought a Triumph instead -- then again, I might not have, it's been a lot of fun getting to know this bike and its quirks, and I'm looking forward to some winter riding in the city.