You ask good questions. You are right. They are two separate bookings. Here's what has happened so far:

1. I emailed Garuda's customer service email ([email protected]) and asked them to add a note about my onward flight (with all details) to my Garuda reservation. They emailed back within a few hours confirming that they had done so and sent me a screenshot. As such, I'm feeling confident Garuda will check the bags onto the other flights. If somehow I get an agent who refuses to do this, then the back up plan in Bali is to put some money in my passport and hand it back to the agent. From past experience and what Balinese friends tell me, this doesn't cause offense and usually resolves all problems.

2. I will do online check in while in DPS for the JAL flight. It appears I can travel between terminals at NRT without passing through Japanese immigration, just a transit security check. The shuttle bus is about 10 minutes. This should make the transit fairly quick.

3. What if the Garuda flight is delayed so much that I'm going to miss the NRT connection? I hadn't given that much thought but now I will. If the Garuda flight is more than 1 hour late in departing, then I will call AA and cancel the award and redeposit the miles. Then I'll get a Y award (no C available) on UA's flight at 17:00 from NRT to IAD, and sit in Y for the whole flight thinking it really s*cks to sit in Y, but that's life

I hope that doesn't happen but it's good you mentioned it. That'll be my backup plan.