Hello Mr. Filth,
I'm very glad you're getting a lot out of the tutorial!
It sounds like you understand the process fine, but having more synths than inputs does complicate things a bit because, as you said, the idea is to record the test sound from all the modules in the one pass - so that pass-to-pass jitter is taken out of the equation.
There are probably other ways to work around this, but this is what comes to mind now:
1) Break your instruments down into two groups, say one of 16 and one of the remainder.
2) Run the test, as outlined in the videos, to set the Track Delay for the first group so that they all playback in sync.
3) Choose the instrument from the first group that displayed the least note-to-note jitter (let's call this instrument "Steady Eddie") and add it to the second group. Leave Steady Eddie's Track Delay as it was set in the previous test, don't reset it to zero.
4) Run the test on these instruments, adjusting all Track Delays (including Eddie's if needed) to sync to the most-latent instrument of this group.
5) If, in step 4, you didn't need to adjust Eddie's Track Delay (that is Eddie was the most-latent instrument), then you are ready to move on to adjusting the All MIDI Output Delay. If you did need to adjust Eddie's Track Delay, then add that adjustment to the Track Delay of each of group one's instruments.
6) Out of all your instruments, choose the one that displayed the least note-to-note jitter (this will be Eddie, unless another proved steadier in group two) and use it to set the All MIDI Output Delay as shown in the video. (Note that the All MIDI Output Delay will delay the output of both your interfaces equally, which is what we want, as the individual instruments are in sync with each other already. There's no need to do anything special here.)
7) Now you are done!
The only other thing to add is to make sure you watch and understand video 48, "Bug Shop - Part 3", preferably before running the test yourself. There seems to be a nasty bug when using track delays set in ms, which this video shows how to work around.
Sounds like you've got a great setup, so good luck and I hope this all works out for you.