Well, first the good news... you can safely upgrade from a January version of WPMU to RC4 without too much pain - I know I've done it / am doing it.
The not so good news is that the bigger your site the more of a pain it is.
It seems like the speed of the Site Admin auto upgrade script caller is directly proportional to teh size of your site - for example I've had uniblogs.org (1 Gig SQL) upgrade running for a couple of hours now an it's upgraded 1730 sites... whereas learnerblogs.org (on the same server and with the same config) but with a 4 Gig database - is only on 400.
But I thought I could be clever and direct users to maintenance screen while giving the upgrade all the cpu grunt it needed by putting this at the start of my .htaccess to allow only me to access the site and send other people off to a maintenance page:
RewriteCond %{REMOTE_ADDR} !220.234.169.04
RewriteCond %{REQUEST_URI} !^/maintenance.html
RewriteRule ^(.*)$ http://incsub.org/learnerblogs/maintenance.html [r=301,L]
And it worked!
In that it allowed only my IP to access it... when I went to run the upgrade script it ran like a beauty (dead fast too) but without, um, upgrading anything.
So I'm back where I started - blogs giving errors over a 24 hr+ period while the script plugs through them :(
And that's just learnerblogs... edublogs is going to be a completely different kettle of fish.
Any suggestions / ideas?
Cheers, James