wait so im assuming everything on the commons area of the footswitch should be grounded, so that would be including the tip of both the input/output jacks?
The middle pins on a switch are only called common, because they are always connected to either the pin above or below.
If the tip of the jack is grounded, the signal will go to ground, meaning no output. Some switching systems ground the circuit input when it's switched off to reduce noise and other issues, they never ground jack tips.
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Are you 100% sure that both of your jacks are functioning as they should be? It is possible to twist them and mess with connections (I've done this once before). As mentioned, there's still a possibility that they are touching the enclosure.
I think you are going around in circles at this stage. I would suggest;
1) desoldering the jacks and stomp switch, test the jacks and switches
2) make sure the circuit actually works, which I don't believe you have done yet
3) redo your off board wiring, and make sure it passes signal when bypassed
4) put it all back together now that you know you have a working circuit, and switching system