Okay, I muxed together the audio and subtitle file with the Japanese BD's video stream in TSMuxer and they match up perfectly. Great work, Matt!
I then threw that into Clown BD and was able to re-author it with forced subtitles. Just to make sure nothing funny had happened, I replaced Clown's a/v stream with the original TSMuxer one. The subs still came on automatically.
I've uploaded Clown BD's file structure for anyone who wishes to use it. Simply paste TSMuxer's "00000.m2ts" file into the BDMV>STREAM folder and you'll have forced subtitles.
[link removed]
This also incorporates the chapter list from the Japanese BD.
Thanks again, Matt!