This looks to be a very nice product and has quite a lot of features packed into it. I recently finished a project with an ESS which used all 3 ports communicating with both 5V and 24V signals. It required 2 breakout boards, 2 signal voltage translator boards, 6 external relays, and a lot of panel space. I bet I could have accomplished this with only the board shown above and 3-4 external relays.
My only concern would be the use of solder jumpers throughout. This is great for the hobbyist (especially those who regularly work with PCB's), but industrial customers may prefer banks of DIP switches, even if that added to the cost slightly.
Your manual seems to be well written and complete. The explanation of various pin functions can be a touch confusing, but all the information is there.
Nice Work!