I attempted to create a patch in October, 2017 with success, and I've just finished reverse-engineering my process to share it with you.
Originally, I found a file by Tom that was very helpful, and saved it to How-To_Manage-Patch-Banks-With-The-MT-32!.txt. It started me in the right direction, so I'm linking a .7z archive including it, the DOS and windows tools, my working files and a couple screenshots for illustration:
https://drive.google.com/file/d/1mAXIV8 ... sp=sharing
The first thing I did, was use Dr. T's MT-32 Editor/Librarian to create a patch in Tom's empty patch bank template. After creating, and auditioning it to my satisfaction, I clicked "patches" in Dr. T. There I picked program 27, although you can probably use any (after you change the leading "A", "B", or "R" to "M"). Next just drag the "M##:" to select your user patch name. Before closing the "Patches" window, note the "midi prog" # (not the number prefixed with the "M", but the leftmost column on the "Patches" window) you've chosen to have your user sound on, as you need to use it later to recall it in your MIDI file/sequencer. Now it should be enough to save your file and quit Dr. T.
Next, convert the .M32 file Dr T just saved to a SysEx file, using mt2syx on windows (or wine).
Finally, import the SysEx into your sequencer, and make sure whatever channel you want to play the user patch on (2-8), has a program change set to the same PC# that Dr. T had as the "midi prog" # noted earlier from the "Patches" window. If your sequencer uses hexadecimal numbering (as MIDI files do internally), 0 will correspond to Dr. T's numbering of 1, and you will need to subtract one from the number you noted. Most likely it will number from 1, just like Dr. T, and you can use its same number.
For my use, I created a separate SysEx midi file, to be played before the song, but you could just embed it all in the song file if you'd like. The SysEx generated by Dr. T is rather a lot, but I'm sure you could examine it to glean the specific few messages you'd need, if you wanted it sent quicker. It's fast enough for me to send it all, though, at about 6 seconds. Just be sure the SysEx is sent before the song starts playing the channel with your user patch (and probably before the needed program change occurs).
I did all this, trying to recreate a complete "Raptor: Call of the Shadows" soundtrack for the CM-64 with the SN-U110-07 Electric Guitar card, but noticed in June of 2018 that Tom had a reverse cymbal programmed in ecoed11.mid on channel 1 of the SC-8850, so the original Eco Quest track should have had one too. I still haven't compared them, though. Nevertheless, it provided a good learning opportunity for me, so it's probably good to have discovered that later.
Since you thought it might have been a problem with the original MT-32, I just tested that my MT-32 (old, 1.07, 10oct87) has "ReverseCym" set on part 2 (midi channel 3), and it sounds correct. That shouldn't be all that surprising, though, as this is likely very similar to how many old games did it. Not being able to support writes on the original revision MT-32s would mean games would really have had to hack it to program their sounds. I know they exploited bugs, but I doubt that such a hurdle would have allowed the synthesizer to become quite so popular.
I hope that helps, and I'm sorry I didn't notice your question earlier.