OK, this is too easy.
1.
Make sure your iDisk is syncing properly. Open finder window and click right ON the double arrow next to your iDisk. It will say "syncing iDisk, checking items" for awhile, then it will sync some items, then it should say "Last sync: [current date/time]." If you get errors, run it again. Reboot if necessary and repeat.
2.
Backup and Sync OF. Open OmniFocus on desktop, go to Preferences, General, Backup, check "Also Backup While Quitting," and then EXIT OmniFocus to back up your database; then reopen it. Now go back to Preferences, go to Sync, and sync. While you're syncing, quickly open a Finder window, select your iDisk, and watch it while syncing to make sure it syncs. Close OmniFocus.
3.
Rename iDisk Database. Open a Finder window, go to your iDisk location where "OmniFocus.ofocus" is, and rename it to something else.
4.
Resync. Reopen OmniFocus on desktop, go to Preferences, Sync, and sync. This is going to create a new OmniFocus.ofocus file on MobileMe. You will NOT see it right away locally on your Mac; you'll have to sync your iDisk before it shows up.
5.
Reset Your iPhone Database. Go to OF on iPhone, Settings, and tap "Reset Database". That should wipe the iPhone OF of data. Now see if you can do a sync. At some point OF may ask "Sync from local data or server?" Say server.
This is pretty much what I did to fix things. My syncing time on my iPhone dropped from 10-15 mins to 40 seconds. The size of my OmniFocus.ofocus file on MobileMe dropped from 3 GB to 56K. Subsequent syncing of the iPhone over wifi takes 5 seconds.
The only thing I omitted from the above was a script called "coalescedatabase.scpt" that I ran before the whole procedure (provided by OG). I don't really think that helped, since I renamed the database anyway, but if you want the script, it's here:
http://www.the-iblog.com/2008/08/05/...-possible-fix/
If anyone has any complaints, additions, revisions, etc. to the above, please post. I know a lot of people having been going through pain over this, so getting a quick, easy fix in place before the next update comes out is worth some collaborative effort.
Thanks to the-iblog.com and Monica at OG for all their help!