Hi Eric-
The Arduino and Shopbot are two of my favorite toys! (Especially the ARM based Arduino's like the Due.)
Shopbot unfortunately does not provide a built-in interface to auxiliary controllers like an Arduino. That does not mean you cant outwit it and do it through the back door.
One way would be to implement a synchronous serial link using 2 of the TTL outputs. One for clock, one for data. Then a short subroutine in the SBP file can output commands over the cobbled up protocol link.
Another way is talk to an Arduino is to write a communications program that has to be run in parallel with the SB3 program. Shopbot does allow communication through the PC registry. That is also very klunky but its at least supported by the SB3 software directly. That is documented in the SB programming documentation. SB3 does not provide any mechanism to launch your program however, so do it the other way. Launch your program and have it launch SB3.
Its a real shame the "open SBP" format does not allow user defined functions, as that would allow convenient calling of your subroutine, but again you can simulate it by using a set of global variables to hold the calling parameters. (I have had to use this method for some of my "active" SBP files.)
Lastly there is the issue of changing the post processor(s) to call your laser controller for "cut" or "engrave" settings. Impliment any protocol you like on top of either of the above communications methods.
I have advocated using UDP communications between the host and ShopBot, that would allow any number of intelligent controllers, but no support has been provided. Arduino's love UDP (so does everything except shopbots), as the Wiznet 5100 chip they use implements network communications in hardware, including TCP/IP connections. If you tinker any at the low level, check out that chip, it makes life so easy and is hacker proof, since hackers cannot change the hardware! Get a network shield and see what they are doing.
That is probably information overload, but that might help get you going. Sounds like a cool project! Keep us up to date.
(A fair note of caution, using a Laser on a shopbot is risky, as there is no safety mechanisms appropriate for high powered lasers built-in. Between glints, toxic exhaust issues, and eye safety, among others.)
Hope that helped-
D
"The best thing about building something new is either you succeed or learn something. Its a win-win situation."
--Greg Westbrook