We are currently running a bill acceptor on a pc.
A bill acceptor is hardware. How can you run that on a PC. Software runs on a PC.
That software might interface with some hardware (like a bill acceptor). So, what software are you running? Why does that program "send a ~"? Can you change what it sends?
We would like to hook up the bill acceptor to the arduino.
That might be possible, depending on the mysterious bill acceptor.
Can the board do this
The Leonardo can emulate a keyboard, as can the DUE.
and is there information here about how to do it?
I'm sure that there is.