Hey, just plopping this thread in here even though I've already solved it for the next person that has this issue: If you have an issue wherein your battery light is on for the first few minutes on the first startup of the day, but eventually turns off, you likely need to either rebuild or replace your alternator. This was a bit of an odd one to diagnose because, A. after the first startup of the day, it wouldn't happen until the next day, and B. at least in the beginning, once the alternator started charging, it worked great and the whole situation was like it never happened. I originally suspected an issue with the ELD (electric load detector), but the issue continued after disconnecting (here's how to disconnect it if you want to do this as a test). Gradually, it will get worse and the 2 minutes it takes for the alternator to start charging will turn into 10 minutes and eventually longer and longer, the whole while your battery discharging and various systems of your vehicle dropping out as you drive. To summarize, if you have these symptoms and have already looked and confirmed your battery connections are clean and tight and checked the connections between the alternator and battery, replace the alternator.

 

@Jared592: Thanks for the heads-up post.

doctor j is our in-house alternator guru. Maybe he will see this.

 

Failing ELD will set a CEL code in memory (CEL will be off) and will cause steady 13V when idling in drive (a/t) with lights and heater off (it normally goes down to 12 volts, unless battery is discharged).
This situation points to worn to minimal length alternator brushes or cold solder joint on regulator (I've posted photo a while ago ; all components of the alternator are soldered together, not bolted together like on older Toyota alternators)

 

Yep, my suspicion is that it was a cracked solder joint that was making intermittent connection and would regain continuity after a certain temp was reached. As heat cycling continued over time, it slowly got worse. It also took longer to start charging the colder the temperatures were.

I was planning on rebuilding it, but, when removing the case bolts, 2 of the 4 snapped off (things get rusty here) and it was looking like it was going to fight me the whole way, so I just replaced the alternator instead.