So, where I stand now. I ended up using a Mesa 5i25 PCI card and a 7i76 step/dir control card. The Yaskawa servos have pretty good auto tune so I decided to leave the PID loop up to the servo drives.
Speaking of servo drives, that and the servo motors were about the only things I kept from the original retrofit attempt. I even had to replace the couplers to the ball screws. A word of warning, do NOT use helical couplers with servos. They are very springy and will make tuning a nightmare if not impossible. Use bellows or disc style couplers. They are the only couplers rigid enough for servos.
The laser is controlled though about 30 I/O lines and I am using Opto22 modules controlled though another Mesa board to handle all of that. In the end I plan on being able to set the pulse rep rate, width, and height through LinuxCNC. Each parameter uses 8 bits to control it and is selected through BCD on the first and last half of the byte. So 65 would be 01100101 with 99 being max and 0 being minimum. The logic is all 15v to the Opto22 modules work out real well to interface.
The laser is running pretty well, I am getting about 200 watts out of it as it sits. The rod needs to be refurbished and it needs new flash lamps. For welding the laser is configured in TEM Multimode which gives max power and crummy beam quality which is fine for welding. There are optional optics which can be installed to make the laser TEM00 and drops the power down to about 120 watts average. In this mode the laser can cut though about 5mm of metal.