Here's where we started, a temporary 'proof of concept' adapter harness from the FJ60 to the FJ62 alternator:
The concept worked perfectly. Since there is no reason to go back to the FJ60 alt, the 60 connector will be cut off and replaced with the 3FE connector. The 3FE alternator plug has 3 terminals vs the FJ60 2 terminals. They are IG at the top (+12V IGnition power), S at the 3o'clock (Senses chassis voltage, tries to keep it at ~14V), and L at the bottom (turns on charge Light if alt is not charging).
Electrically, the only difference is the additional S terminal at the top. It can simply be connected to the +B post with a large ring terminal, as the factory does in the FJ62 harness.
The black FJ60 IG wire should be connected the center IG terminal.
The white FJ60 L wire is connected to the bottom L termianl
Wires ready to be crimped together.
The rubber boot on the smaller 2F connector is the same OD as the new connector, so it gets taped to the end of the connector, it won't actually slide over the connector. It's better than nothing.
After crimping & taping, the 3FE connector from Coolerman fits perfect in the back of the alternator.