So many questions.
Your TTL switching of the laser is probably best done by setting Output#2 to Port 1 Pin 17 then within the Gcode using the M11P2 command to switch the laser ON and the M10P2 command to switch the laser OFF. These commands can be automatically inserted into you Gcode by modifying the standard BobCad post processor (check with BobCad – they have already modified a post processor for someone else). The M11/M10 commands only take effect upon axis movement so they are fast acting and work well for me.
If you are looking at software other than BobCad then check out PicLaser
http://www.picengrave.com/ also look at their methods of laser control etc.
Tweakie.