Success!

Update: I was able to get a file to load and play! I was just sure to include all the values outlined in the BIFF. From what I can see, the chunk of data that follows a VAG file in the BJS is optional, as long as I set its length to 0. I just hope this doesn't break anything in the future.

On another note, FreePlay and I have been desperately trying to figure out the unknown values found in the header of BAR files. From what it looks like, they're related to the file name, as the manifests always have the same value, but the others change per the name of the folder. If we figure out out to encode our own names, it'll be possible to add content to Beats as opposed to replacing it.
I hand-built a really simple BJS with only one loop in it. It loads, counts off at the right tempo... then freezes. I didn't add the unknown data that would normally follow the VAG, so that might just have something to do with it.
Interestingly, I couldn't name my folder JAM_0000. Renaming it to JAM_0002 works, but means one has to replace a song.

Be sure to check out FreePlay's excellent "unbeat" tool for extracting BAR files. A lot cleaner and faster than using File Juicer or doing it by hand.