I’m sorry to read about your problems. I had a MIDI Clock problem before but I solved it when I replaced a Timeline with a Boss DD-500.
What happens if you get rid of the thru box and daisy chain all of your pedals? Just make sure to have anything but your H9s first in the chain; Eventide stompboxes are well known for not the doing the MIDI thru job very well. The Strymons will do it right.
Have you tried using the same cables that you are using for the Strymons and the Echolution?
By the way, do you know you could use your H9 as a MIDI clock source?