The trees were located in dixie:~/Projects/EPI/repo/ and still are. After backing up the repositories, I created a new 'work' tree to become the home of this merger, threw them together, and did some clean up. First I tried using git filter-branch and git format-patch together with a few other mungies to get the history retained how I wanted it, then I decided to screw it and just make branches reflect the history—even better then what I wanted.
I then used git format-patch to create patch sets, placing them in temporary directories. Rather then change the patch sets to reflect the merge (good task for perl scripting), I decided to rely on git mv for something more full proof then hacking patch files by hashed out automata.
Creating a new 'work' repository, I made an initial commit with a stub file, then created suitable branches for each in my original repos, which is a task easily automated in sh or Perl, for people with lots of branches. A little bit of git checkout and git am, then slurped up the patch sets bringing each repository (and it's associated branches) under one roof.
Creating the new merged 'master' was a simple octopus merge.
$ git checkout master $ git merge repo1 repo2 ... $ git mv ... $ git commit -a
Job done, good night!
Note also, I wanted the trees merged, so conflicts were not even present, hehe.