It sounds like your main goal is to use MIDI out from the pi-Stomp (USB or TRS) to control your amp, right?
I have to admit that the main focus for the MIDI offerings on pi-Stomp have been as a receiver of MIDI messages, not sender. That said, Alsa is quite powerful and configurable, so you should be able to achieve that.
1) Does the midi-out on the add on board work when using the usb port to receive midi-in signals?
The two should be independent.
2) Does the expression pedal also connect to other devices when using the same out port?
The expression pedal input is used as a MIDI CC control configured via default_config.yml (MIDI chan, CC message, etc.) Alsa will recognize it as a MIDI device which you should be able to use to control other applications running on the pi. It should be routable to other MIDI devices via ALSA. If you're asking can it be routed out of the pi-Stomp to control another physical device, I've not tried that, but it seems like it should be possible.
3) Can the output port send a signal via USB or do I need to use the 1/8" jack to 5-pin midi adapter and then another adapter to USB.
USB MIDI is a separate device (with input and output) than the serial MIDI device that the MIDI+Exp board offers. You should be able to route between the two via Alsa, but again, I've not tried.