I’ve found the Migration Assistant to be solid—almost fanatical—for persisting custom settings. Most recently, it carried over my non-standard OpenSSH + config with resident key support, GPG config, and a couple of other things without a hitch. I even found a few config files from 2007 and a same-era Safari SIMBL extension that probably stopped working in Snow Leopard, all faithfully migrated across five different machines and a dozen operating systems.
You know, it's probably not migration assistant. I would say it's a major OS upgrade and gets tarred with the same brush. I personally have found it to be fantastic for upgrading to new hardware.
I’m curious what doesn’t work for her.