Jim_J:
I'm not sure I have made it clear what I am trying to do (if so, I apologize for my lack of clarity)
I guess not.
Try again.
Maybe a diagram would help.
If space is at a premium why not make a standalone Atmega 328 on a piece of stripboard. You can use a USB-TTL cable to communicate with it.
And, of course, you could use a USB-TTL cable to communicate with any of the pins on an Uno. But keep in mind that the USART is only on Pins 0 and 1.
...R