So you have just a power and a ground? One to the battery positive and one to the engine block? I'm sorry, I may be thinking of a different setup.
If that's the case, I would make sure the wires coming off the alternator can carry current. Try this, start the engine and take a voltage measurement between battery negative and the positive post on the alternator. If the alternator is trying to charge the battery, it should be higher than battery voltage, somewhere around 14 volts or so. You can also take voltage measurements between the battery positive post and the positive post on the alternator. The reading should be roughly zero. If you get a reading much higher than zero, the wire is unable to carry current. You can do the same with the ground wire. Take a measurement between battery ground and the ground on the alternator. If you get more than a zero reading on either of these, the cable is probably bad or has a bad connection.

 

As far as I know, there's nothing unusual about the wiring of my alternator. The replacement one I got last year bolted right on, and everything matches the wiring schematics in the RAVE. One positive, one signal, and ground through the alternator chassis. There's no negative wire going to the alternator itself.

 

An update on this -- I'm still struggling with it as I've been pretty busy lately.
I discovered the other day that none of my accessories function in the #2 key position without the engine running. I assume this is related somehow to the non-charging situation but I haven't been able to track down any specific wiring that might cause both of them. I have been going over every ground connection and cleaning them. I installed a brand new battery. Nothing has made a difference.
I only noticed both issues after I replaced the head gaskets, during which process I had all the appropriate wiring disconnected or unbolted. I can't find anything that I didn't reconnect.

 

Are you sure you didn't miss a ground from the body to the engine?
Maybe try checking for power on the fuses for some of the accessories that aren't working. If there's no power maybe something in the ignition switch isn't making contact.

 

Not the ignition switch, as everything works correctly after the engine is running and the key has returned to position #2. There doesn't seem to be anything common between all the things that don't work aside from that they're supposed to work. So far I've noticed wipers and washers front and rear, radio, and power seats. All work fine when the engine is running.

 

Check your under the hood fuse block and check the 150AMP strip of metal/fuse. It could be blown. I carry a spare in my roadside kit.

Also you could test the positive lead to the alternator by using one side of a set of jumper cables. Attach it to the alternator then the positive side of the battery. If your voltage goes up to 13.5-14.0 then it's now charging. If no change that's probably not the issue.

 

I've had the 150A fusible link go out before (positive cable shorted against the exhaust manifold) and these symptoms are different. But I'll double-check just the same.
Nice idea on the jumper cables. I might try both pos and neg from the alternator straight to the battery terminals.

 

The alternator has one lead and that's + it gets it's - from the engine mount or actual metal assembly of the alternator. The brownish colored wire from the alternator runs directly to the under the hood fuse block, then a lead goes directly to the battery if I'm not mistaken.

 

Yes, I know. I would attach the negative jumper cable to the frame of the alternator and the positive cable to the terminal, making direct connections to the battery and thereby eliminating any flaky ground issues. I'm really in the dark on this so being able to definitively narrow it down to a bad ground would be a huge step forward.

 

You could try putting a jumper cable from battery negative to the frame and/or engine and see if things come back to life. I've see dual battery systems stop charging one battery because of a bad ground to either the frame or the engine. Just a thought.