Update: I've resolved the problem I was having (a config file was still pointing to the old site directory so all my included files were coming from the old 1.3.8a site, doh!).
All the same, if anyone can sanity check the steps I took I'd appreciate it. I don't really understand why I needed "git add" and "git commit -a" at each step, for a start.
PS: Apologies to MJR, I messed up the to/cc on the last email. Thunderbird no longer recognises my list email now it goes through an Exchange server, grrr....