Oh, and yeah, it sounds like you've got the right idea with the MIDI Merge box. Most of the merge boxes I've seen are pretty small, so hopefully, you could strap it underneath your pedalboard.
Sounds like you've got quite the rig… I've recently split my pedalboard in two, as you describe, keeping all non-time-based effects on one board and all time-based effects on the other. Sounds like it's for the same reasons, too. I switch amps a lot, too, some with loops, some without, and some rackmounted, and splitting the board like that has been more flexible, too.
BTW, Badmelonfarmer, I took a look at your diagram and that makes a lot of sense. Sounds like you've got a pretty impressive rig, too.
And thanks for the input on the Eclipse vs. H8000. I've been debating that myself. Still not sure what I'll do there, though. I'm primarily a guitarist, so the Eclipse makes a lot of sense. But, I have a project studio, too (mostly local church groups and bluegrass, but some rock as well), so I can definitely see the H8000. Given my recently diagnosed addiction to and penchant for acquiring Eventide gear, I wouldn't be surprised if I end up with both, too, at least at some point.
