Tricky stuff - and welcome Chris. I am not sure which motor or alternator that you have, but this does sound like a problem with the alternator - the rectifier or regulator circuits. I am by no means a specialist, so would suggest that you take it to your local auto-electrician and have it checked out. This may help in the meantime if it is a Ford one.
http://fordfuelinjection.com/?p=63
Merv