It looks like your making some major progress.
We just set up a 3040 Parallel Port CNC machines like this one and controlling it with an Arduino UNO R3 flashed with the MultiMode 1.0c grbl firmware.
We did not have to modify/change anything in the controller box at all. We did have to change pin numbers around from a DB25 Arduino Shield to the controller with a DB25 Jumper box. We have a DB25 Y splitter cable coming from the Jumper box to a DB25 screw terminal breakout board for connecting the PWM output to the laser driver. We have it running with a WinXP Pro, Pentium 4 3.0Ghz processor, 2Gb of ram PC and the PicEngrave gcode files are being streamed to grbl with our PicSender program. Can't get much simpler than that and It all works perfectly.
Here was our first try on Birch Ply with our J-Tech 2.8W laser.
The PEP6 Analog/PWM settings were:
Engraving Angle: Left 45D
Pixel Resolution: .007"
Max. 3rd Axis Depth: 255
Min. 3rd Axis Depth: 5
Feed Rate Change: 25%
Extended Edge: 20 Width in Pixels at 73 IPM