Looked at their site and cant find any info on that. With you saying its a card then I would suspect its an analogue amplifier so you only have a few options if you want to keep them. One is to try some of the Analogue to Step/Dir converter cards, dont have any experience of them and the reports of them are thin on the ground.
Another option would be the DSPMC motion controller, have seen a few recent reports and they are all great. Problem is its around $800 I think.
You could also get the likes of Gecko G320'S or CNC Teknix Tek10's to replace your drives. You would lose speed though as the max voltage they can handle is 80v. With your figures above that would mean your motor speed would be limmited to around 1,300 RPM.
Personally I would go the DSPMC route as it would allow your full speed and also no problems with the highish count on the encoder. If you went one of the other routes then your max speed with 1000 count encoders would be limited through the parallel port, at 45KHz you would get a max of 675RPM, so you would need to go for a 100KHz kernel speed to get the 1,300 rpm the geckos/teknix would allow. Whether you can get 100KHz from your port is highly dependant on the computer.
You could of course go the SmoothStepper route with Geckos or Tek10s. The SmoothStepper does the pulsing externally from the computer and has a max of 4MHz, I use the SmoothStepper on all my machines
Hood