Your jack config is likely too CPU intensive for anything except a very small pedalboard. I would recommend trying these:
-r 48000 -p 128
But that's still probably not the root cause. I agree it sounds like the input never makes it to the the sound card, or if it does, it's not making it to MOD.
I just made a quick fix to allow the host test mode (added for v2 by BenH) to also work (mostly) for v1 hardware. You can use it to see if your audioinjector is receiving any audio.
Here's what to do...
First make sure your input gain is high-ish.
Then, via a network connected SSH session:
cd ~/pi-stomp
git pull
sudo systemctl stop mod-ala-pi-stomp jack
(That might take a while)
ps-run --host test
That'll bring up a curses UI. With your instrument cranked, play it and look for VU meter type action next to the L or R Capture fields.
If you see segments "lighting up", then the audio card is receiving output and we'll try to figure out why MOD doesn't appear to be receiving it. If no segments, then I'm suspecting a hardware problem. Let me know, and we'll go from there.