you might be overcomplicating it if thats what you want (locate which buffer each pin belongs to). Im thinking about also replacing some of these at some point but may use parport for inputs and just use this board for outputs and step generation in immediate future.
What I would do is use digital multimeter on continuity test mode on a known pin say, pin 1 on connector J16, have one lead connected to this pin from the multi meter, then sweep remaining lead across the buffer near that connector on bottom side of board, should be pretty easy to locate which buffer has that pin.
One thing to note is that on the J connectors, only pins 1,2,3,5,6,7 are connected to the buffers. the rest of the pins on each connector are 'shared' with the same fpga pins, you can see this in the connector mapping in the file you linked above.