Some time ago I read a thread on here about how to wire up a trunk mounted battery so the main cable to the starter was only live during cranking. I think it used a ford solenoid. Does anyone have a diagram on such a set up? How does that set up work with the alternator putting juice back in to the system? Does the alternator require a separate lead to keep juice out of the battery cable?

you should be able to find something here.
http://www.painlessperformance.com/manuals.php

You use a Ford solenoid out back, close to battery with fusible link protection. Have to run heavy charge wire to battery as well. I think you are referring to the diagrams from Mark at MAD ELECTRICAL. Try madelectrical.com

I have a diagram so the alternator wire is only hot when the switch is on. Not sure why you want to kill the main wire to the starter.

Starter line normally cold and alt cold when switch is tossed