I made the effort to post this information to save someone else the maddening experience I just went through as no existing thread clued me in to what happen.

I posted an earlier thread titled Zen and the art of Midlands repair on the rebuild of a failed 5 speed. The side note information came when I put the transmission back in.

Upon reassembly of the car, I started it and the alternator light came on, which it had never done before. I looked everything over and found nothing unusual. Double checked all the connectors, cleaned all the grounds, crank pulley is fine, belts are good so pulled and checked every fuse and found absolutely nothing. I jumped on the forums scouring for anything on this problem and found nothing quite like it.
Having been burned by assuming coincidence equals causation I tried to keep from assuming that it had to be something I did. If this happened without the transmission job I would assume it to be a failed alternator so I pulled it and had it checked. Dang! That wasn't it, tested fine.

I then decided to trace every wire that I touched in the process of removing and reinstalling the transmission. I traced the alternator wires and found nothing. Then I traced the power streering wires and found a spot by the exhaust heat shield that I thought was being cut into by the shield. In the process of trying to get a little slack to examine it a little closer, I couldn't really pull it. I realized that where it ran behind the coolant tube on the back side of the head, I had pinched part of the small bundle of three wires that goes to the power steering pump.

I loosened the bell house and starter bolts to make a gap to pull the harness out and it was then that I could see one of the three wires had been pinched in two. The yellow wire was obviously shorted to ground. After soldering it back together and heat shrinking it, I put the battery back in and presto! It was charging.
If you are doing a trans or clutch be very careful to not do what I did. It was easy to do and impossible to see that I had.

 

Saw that thread, great work. Also, thanks for posting this up as I'm sure someone will appreciate it if they run across the same issue when they do a similar job. Glad you found it and things are working like they should.

 

Good find!!
Great too see you looked for the issue, rather than just tossing $$$ pars at it...
From reading it, it sounds like the wire that got pinched/cut was the wire that provides the tiny bit of power that an alternator amplifies....with old style generators in classic cars
you had to "flash the field" when you I stalked them...then no input needed, but max output was terrible at low rpms...ALTERNATORS are generally superior, but folks forget about the input voltage (most are NOT SELF EXCITING) unless it is a "one wire" retrofitunit....