I have two major problems:
A: Battery is dead. Not charging. Battery terminals are ok. This problem is fairly easy; believe it's the alternator, voltage regulator, and / or associated wiring.

B: Several sub-systems inside the car are not functioning. This problem first surfaced with NOTHING working (no start, no lights, no bells, no nothing). I referred to a wiring diagram I had (but have since lost): Found the 100 AMP ALT fuse blown. Replaced it. Then, I was able to start the car, and was able to drive it for about 3 days. Still have MANY sub-systems not functioning:
1: Tail-lights (but headlights are ok).
2: Brake-lights.
3: Turn signals (but emergency flashers are ok).
4: Power seats
5: Power mirrors
6: AC blower
7: Clock
8: Speedometer, Tach, Temp, some indicators. Oddly, the gas gauge appears to be working. 3 indicators ARE working: SRS Fault, Door(s) open, Seatbelt warning bell. No other indicator lights will turn on when starting, or when the car is running.
9: all dash board lighting / dimmer rheostat is not working (but courtesy door, dome, and visor mirrors are ok).

I replaced the AM1 30A fuse, but the symptoms above remained (no change). The only things between AM1 and the ALT fuse, are the ignition switch, and portions of the Integration Relay. The wiring diagram I had indicates everything on the list above goes through the ignition switch, but only the seat, mirror, seatbelts, brakes go through the integration relay (near as I can tell).

We drove the car like this for 3 days, then the battery died. Got a jump. Drove it for two more days. Battery died (hard). Got another jump, but didn't make it more than 2 miles, when the car started to die. No more battery, unable to start. I'm not sure if the alternator / voltage regulator were functioning properly from the beginning, or failed later. (note, however, that the ALT(ernator) fuse was blown at the beginning of the problem.

I'm going to isolate the alternator / voltage regulator failure first, then look into the integration relay / ignition switch ideas.

Everyone: this is the only transportation we have, and we have limited income. Toyota / Lexus mechanics charge $138 / hr for troubleshooting (and I expect they will take 2 or 3 hours to find the problem). Then, it's repair labor and parts after that to get the car fixed. I am an experienced electrician / electronics tech. Give me a wiring diagram and / or a shop manual and a multi-meter, I can find the problem.

If anyone has seen anything like this, please advise. If anyone has a 98 lexus wiring diagram (for free), I'd appreciate a link to it. (I can't find my link to the one I had before).

 

To begin with, look for the easy things. Like maybe the battery is going bad. An internal short inside will draw a lot of current from the alt and could have been what blew your 100A fusible link. Those are pretty stout and don't go down without a fight. Or maybe someone jumpered the battery backwards or shorted the alt main feed to ground. But something drew some serious current.

At this point, I would advise NOT to over-think this thing with wiring diagrams until you have made other more obvious checks. I would be looking at the integrity of the battery first. Get it started again and check the charge voltage with a voltmeter (should be north of 13.5V). Then, with the engine off and headlights on, the battery should droop to about 11.9v and hang in there for quite a long time (10 minutes or more) before slowing heading lower. If it will not hold, your battery is either undercharged or shot. I am guessing shot.

 

Off the bat you probably need a battery. Maybe it can be brought back to life but don't be surprised if its pooched. If the 100Amp fuse blew its a short in the alternator, check the wiring between the alternator and the fuse to make sure its not the cause first..then if its good. Change the alternator and possibly the battery. As for everything else....check every single fuse in the boxes and replace as necessary.

 

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