I had a much longer reply written above (describing my loosely similar setup), but I inadvertently switched pages and lost it.  But it did jokingly add "now all you need is an EHX 8 Step Program slid in after your expression pedal".  It takes up some real estate, but I don't know that I could do without that processor now.

The multiple EXP PED routings can be difficult, but the H9 Control method is miles ahead of the way we did it in the Stompboxes.  I try to concentrate on one at a time, then a pair of routings, then fold in the third …  The visual (virtual) knob direction helps, but I usually know pretty much what I'm after when I'm programming multiple routings in.

Another thing to watch for is the "sync" between H9 Control visual feedback and the actual setting in the pedal itself.  In many algorithms, they're not the same.  For example, you may see EXP PED, but it's actually SAMPHOLD in the pedal.  A little further clockwise, and a visible EXP PED setting shifts to audible EXP PED results.

It's not just 1 or 2 algorithms, or in earlier versions of H9 Control.  In the Looper algo, I'll have AUTOPLAY set and saved in H9 Control, and the pedal will be in a LOOP PlayMode.  I have to bring it to a 3 o'clock position (almost to RE-DIRECT …) to get AUTOPLAY to "stick".