Things learned from the rebuild:

• Build the new install with a user other than yourself (I used hcmc). Then do a bunch of configuration and installs, before creating a new user for yourself, with home dir specified as the (in this case new) home partition. This simplifies things, because you can have the whole system basically up and running before you log in as yourself, and all your settings should basically work out of the box.
• Mount the new home partition at /home/[username] -- this was the original location of the home directory on the root partition, so now scripts etc. work as before.
• When using cp to copy the home dir around, don't forget the -p (preserve) flag. I forgot it, and now all my home folder dirs and files have new dates, which means rsync backups are going to take forever for the first little while.
• Also watch out for cp failing to copy hidden files and folders. Don't know why this was happening, but it was consistent; I had to copy them manually using Nautilus, and even that failed on some folders without reporting any error. Check that source and dest are identical when you're done.
• You'll have to chown -R user:user virtually everything on non-root drives to make all the resources you've been using accessible. That can take a while for a big secondary drive full of media files.