Here's the instructions for smooshing your zip files so it is less likely to time out:
If you don't have a Mac, email
urgent@omnigroup.com and one of our crack ninjas will help sort you out.
If you have a Mac...
Sync all your Macs, then run the attached applescript on whichever one has the most up-to-date info.
(You can run an applescript by opening the "Script Editor" application, opening the script file, and pressing the "Run" button.)
Next, open up your iDisk (or whatever location you're storing your sync database in) and rename its copy of the OmniFocus database to "OmniFocus-Old".
Do a sync from the machine that you ran the applescript on.
Launch OmniFocus on your phone and start a sync; when asked whether to use the 'local' or 'server' copy, choose 'server'.
Your syncs should now take a reasonable amount of time again.