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I have a Superpro Plus and I am running out of pins. I see in the schematic
that TXD3/TDX1/TDX0 are all jumpered together, same goes for the RDX's. I know
that TDX0/RDX0 are for the programming interface so I don't want to mess with
them but I want to use the others for GPOI. Can I do this on this board?

R9 through R11 are not loaded (they would be on the circuit(back) side of the
board. And would allow a different UART to be connected to the USB serial port.
So you can use TXD1, TXD3, RXD1, RXD3.