Here is the process for customizing the MOTM-650's tuning table with your own tunings (using a mac). If you found this page that was the hard part, the process is actually quite easy. The MOTM-650 uses Midi Tuning Standard (MTS), which was designed by Robert Rich back in the early 90s. You just need a simple program to write MTS files, and transfer them into the 650.
The Process on Mac:
Download Max Magic Microtuner (MMMT), and get a license.
Connect a Midi In/Out interface to your mac (something simple like the M-Audio Uno will work), and connect the in/out cables to the MOTM-650.
Open MMMT, and select your Midi interface on the Midi Settings Palette, from the drop down list.
Now create a custom tuning using the MMMT program (you might need to read the instructions).
Alternately, if you are like me and find MMMT excessive, you can import a standard Scala (.scl) tuning file into MMMT. Just click the "Import SCL" button. Make sure the "Expand at Load" box is checked so that your scale expands to cover all octaves. If you don't know, a scala file is a very simple text file, it's just a list of pitch ratios, or cents.
Finally, send the tuning from MMMT to the MOTM-650. From the Midi Settings Palette click "Send tuning via SysEx". A box will come up with a few options. Leave everything alone except 1) select the tuning program number you want to overwrite [you can't overwrite #0 equal temperament, so start your tunings at #1], and 2) type in an eight character name. Click send.
Your new tuning should now be in the MOTM-650!