Hi!
I just drew a diagram (used free Figma app) based on your setup (see pictures below).
Since I have no experience with SPDIF and AES In and Outs, this might me a good solution for you.
If you have this type of setup, this allows you to put any pedal between the guitar signal and the amp. (first row on Axe-Edit),
and you can add any pedal to the dry (return) signal. (middle row on Axe-Edit),
and of course you can put in any timed pedal before going to Eventide. (last row on Axe-Edit).
GCX or RJM Effect switcher may give you the option to put your real stomp box pedals before Axe-Fx and you can switch any pedal using a MIDI connection.
Yes, TC2290 has 5 analog loops (4 mono and 1 stereo) but you can only use them right after TC2290 delays. So, you are not allowed to change the order to use these loops before TC2290. I mean you can only have a setup like; Guitar -> TC2290 -> TC's loops -> Amp, you can't use TC's loops before TC2290 itself. I only use the TC's loops for the SPX-90 as the GCX never runs out of loops and I never use time based pedals on the GCX.
Btw, buying an Eventide H9000 is a huge investment. Have fun with it