Luiz, you could add a differential line driver between the BOB and the AB drive. This will convert your single ended Step and direction signals to Step + and Step - Direction + and Direction -. I don't know of any BOBs right now that offer double ended outputs for step and direction. It should work fine single ended but I think the biggest advantage in making it differential would be noise immunity. As far as the encoder for the job, this will effect your resolution and I wouldn't want to go higher than 35KHz with a parallel port which will in turn limit your speed. Mach can go to 100KHz but if the hardware your using (PC/BOB) can pull it off or not is another story. I would look at the Smooth Stepper and a differential line driver.
http://www.warp9td.com/index.php and I saw some line drivers on ebay a while back. I'm setting up a lathe right now with AB drives and motors and this is the hardware I'll be using.
Brett