The description you provide doesn't make sense to me either. There is a simplified schematic of the Ford 38 Amp alternator system on the Technical Data page of this web site.
http://www.337skymaster.com/techdata.htm
Then click on Electrical System Schematic (PCX Format).
You will probably find that one easier to follow than the one in the Skymaster manual.
Can you provide any further description of the problem? Does the electrical system shut down when you turn off the master switch and then come back on? Does it just stay on? If it comes back on, how long does it stay off? Is the problem intermittent?
Also, what position is your 'RUN/STBY' switch in?
What is your Aircraft serial number?