It seems that the issues have gone away now.

I have bought a spindlev4 board to control my spindle, then powered up my BOB with a PSU, and blew the microcontroller on the BOB handheld controller. The spindle board is fine as wasnt connected.

I then bought a new BOB which comes with the spindle output control and relay so im just going to fit that instead.
The Yaskawa relay will be bipassed for the time being (or maybe not depending on if i want to use it in the end). I am wiring in the new BOB and tested it.

Another thing i knew but forgot to remember was that mach3 doesnt like 64 bit machines, nor vista running 64bit, so a few days of tinkering and it was just the PC!
windows 7 32bit now installed and all running ok on a test motor.

Progress will be reported on in my blog, which i will link here when i have done it (although im sure i should rename this post to reflect it as a boxford 260 vmc retrofit)