I love Michael's kit... shame he went over to the dark side (postfix).
OK, I think the migration stuff is probably pretty easy, but I recommend that you compile qmail and vpopmail as new.
spamassassin, clamav, mysql (try to stay same major version), php, perl, and apache should all be usable from the packages available from your distribution. You would copy across your configuration files (i.e. httpd.conf, php.ini).
qmail/netqmail, vpopmail, qmail-scanner, daemontools, uspci-tools, ezmlm , qmailadmin, and the like should be compiled new (IMHO). You are changing enough against the system libs that you risk stuff not working to your taste.
Depending upon how you cooked up your IMAP (courier), I believe it's in your best interest to compile that new as well.
THEN, you should be able to copy /var/qmail/alias, /var/qmail/control/, /var/qmail/supervise, and other /var/qmail goodies along with /home/vpopmail onto your new system. It's possible that some binary locations change in your 'run' files in supervise, so check those before you launch.
You would also copy over the requisite squirrelmail and vpopmail SQL databases using mysqldump to export them. Do not copy the mysql data/ism files and move them.
Finally, you'll have some stuff in your crontab for maintenance and whatever firewall (and hosts.deny?!) stuff you want in place. Oh, and DNS changes.
In short, the prevailing wisdom is to build the system new and apply your old config stuff.
D.E.R. Management - IT Project Management Consulting