I couldn't understand why the brake light circuit was connected to the alternator (and stayed on when both the master cylinder and handbrake connection and wiring were"perfect").

Maybe someone else will come up with the same issue, so here is the answer from a NASIOC thread:

http://forums.nasioc.com/forums/show....php?t=2263691

Normally the field lead on the back side of the alternator should be close to ground potential when the key is turned on and the engine isn't running. Power from the ignition switch ties to the warning lights and then to the alternator field lead which should be near ground potential and that turns on the warning lights for a test. When the engine is started, the alternator uses the current going through the field circuit to energize the field of the alternator and start the charging action. It also builds up a backfeed voltage on the field lead which turns off the warning lights. The lead isn't at ground potential anymore, until the alternator stops turning or has a problem.