I just checked the template that I have used. Mind you, I have only run one successful test (by chance, it was today).
The template is setup for "PE" environment. My template is not as complex as what you described, but your suggestions sound like a good idea.
I would think that you could add a "Shutdown" action after the profile capture, and then progress from there.
SNIPPET:
Profile Capture ->
Shutdown -> (Pause to switch drive) ->
Reboot to PXE (catches after the PC is restarted) ->
Your imagination is probably better than mine, but a few options as I see it. Testing would be necessary, since I am only visualizing. I'll venture it as a guess, and can try it myself. You don't mind if I steal your idea?