I'll make notes of issues I ran into and the solutions as I go along, but so far I've had two three issues come up when upgrading.
1) When I ran the upgrade, it sort of died before finishing… I refreshed and it told me it was all set. Checked on the main page, and everything seemed to be okay – but when I logged in to start tinkering around with the settings, I couldn't log in completely. I got the dashboard with no navigation and then I clicked on something and all it wanted to do was send me to the profile page – but with nothing showing except "You do not have sufficient permissions to access this page". Googled for a solution and found one on Mark's site. Ran his script, and all was well again.
2) Then I discovered that clicking on the the "previous entries" link at the bottom sent me to a "page can not be found" error page. Google to the rescue – and found one on the WordPress Codex… (scroll ALLLL the way down to "Paged Navigation doesn't work" – There it will tell you that the error I was getting was due to the .htaccess file that WordPress generates. Delete the contents (or at least the wordpress stuff in there) and manually add the code back in from the Options -> Permalinks page. Again, all was well again.
3) This one was really weird. I had a post that was showing up in Firefox but not IE. It was like it didn't exist at all on IE. Wasn't in the source. Try to pull up the post page, and it gives you a 404 error not found. Turns out – and maybe this was because of the glitch during the upgrade – the post didn't have any status indicated. It wasn't marked as "Published", "Draft", or "Private". (The weird thing is that, then WHY did Firefox show it at all?!?) Anyway, clicking the "Published" box and re-saving the post seemed to fix the problem.
If you find any other broken links or errors, etc. – please let me know!