Toyota Repair: 1990 yota 4runner sr5 3.0 v6 Electricity!??!!?, using a digital multimeter, car ignition

Question
Just before leaving work the other day I had rolled down all windows. very hot day, forgot the key in IGN on position for about 45 min. It barely started, but i live close, about one mile. went to give a friend a ride home....no good deed will go unpunished??   no power except for door  panel lights and dome lights. 80A main slo-blow fuse burnt. started to look around and eventually with a test meter on audible (in place of the battery which still has lots of "juice"..ZAP!) disconnected fuse items. all of them!! still had the audible tone. started to really look around and found the "B"terminal on the replaced reman'd alternator to have spun to contact the outer case of the alternator. Oh What have I Done??? The fuse underhood-AM1 "green 40amp slo-blow" continues to announce the short circuit when in place. and if the battery is connected...... I need to go buy another 80amp main fuse. big short circuit. Any Idea what happened??
any and all suggestions workable and appreciated. I have mechanical ability and will be outside troubleshooting all day until I figure it out.. I'm just like that. But electricity is not my art, and If I figure it out it will be by luck...Please, I'm in over my giant head...

Answer
Hi,

Are you using a Digital Multimeter? Are you testing voltage...ohms...continuity? If so, I would recommend a Fluke. It's very clear that you need to find a wiring diagram and start tracing circuits to locate the problem. Unlike the old days, leaving a late model car ignition in the "on" position will not damage electrical components. It sounds like it was just a coincidence that it happened that day. How was it operating prior to this day? Could it be that it has been an ongoing problem and it might be a parasitic load?