... I compiled 100D.100C and put the autoexec.bin and ML-SETUP.fir on the SD card with the ML folder from one of the other packages, but I got a black screen with a red LED when I tried updating firmware.
Yes, that's what I've experienced too.
Since you're able to compile you might try reverting back to revision 13131 (January 7, 2016, Branch: 100D-new-test, update consts) and that should load ML. The problem is that the trash button doesn't bring up the ML menu which is the show stopper.
You're right that the autoexec.bin file is different between the firmware versions but it is best to use "make zip" to bundle all of the necessary files in a zip package just like the nightly builds.
In any case, if you feel up to it you might look into why the trash button isn't working and suggest a fix to nikfreak.