We currently use /scripts/pkgacct for full account backups and transfers, hence my recommendation to use that. Looking at the copyright notice for pkgacct2, that looks very much outdated.
We've fixed many of the issues with HTTP timeouts, but I see no problems with doing things the command line way in this scenario.
There's some further details in doing transfers via the command line in our Backups and Transfers presentation from the 2007 cPanel Conference. You can view the slides from this presentation at:
http://twiki.cpanel.net/twiki/pub/Al..._Transfers.pdf