I did a bit of troubleshooting this weekend. I checked with my multimeter the amperage the lights were drawing on low beam and high beam and then compared this to two other FMTV's. On low beam it was drawing over 7 amps and high beam was about 10.5 amps. I replaced the 3 arm switch with a spare one that I had, although I don't think that was the issue. In the breaker panel there are two different relays, labeled high beam and low beam. Interestingly, they work together and removing either of them means you have neither high nor low beam lights. One of the relays had been replaced with a 24V relay, which I'm not sure the voltage matters too much, but I went ahead and swapped it for the B.O. Drive relay since I don't really use the B.O. lights. With the lights on the relays would get pretty warm. Looking closely at the sockets they plug into, I noticed that one of the contacts from each of the two sockets looked like it was bent open too far, and the plastic piece next to them were discolored (presumably from high heat due to bad connections). I used a small pick to pry the contacts out a little so they would make better contact. The picture shows them before I bent them out some. Notice the brown plastic beside them, when the others are yellow. I also replaced the breaker for the headlights with a standard blade fuse for now, in case that breaker was not making a good connection internally.
On a related note, normal blade fuses fit just fine in case you are missing some breakers. The 12V relays used look to me like standard automotive type, but I haven't confirmed that yet. If you look at the label on the breaker panel cover, notice how the relay schematics show the contacts numbered as 87 and 87A, which sounds very familiar to standard automotive relays. This might be helpful when replacements are needed.