Argh. So I just spent the past couple of hours rewriting the update handler basically from scratch to record its progress in an easily parsed way and handle failures appropriately rather than trying to limp by on the crappy hacked-in retry code from last week... try it out, and for the first time since this started, the update went flawlessly. No timeouts, no retries... whole thing took about four minutes and done.
You might think that's a good thing, but the nub here is that I was thus unable to see if the new retry stuff works at all. Let's hope at least that things keep working and it becomes entirely unnecessary...
For those interested, if something looks funny about the altmeta (like an update was botched),
check the log here. It's pretty straightforward--R/C means it's checking a roster (empire) or character, followed by the ID number (found at the end of your page's url). Each dot represents one try, followed by an 'ok' when it has succeeded.