If you can just use the 1Khz pulse to count then

you can use that to time your circuit by sending a Data signal to an AND chip to turn a certain axis on for a number of counts. The circuit could be set up for the frequencies you need for each axis using other oscillators if necessary. 555 chips generate nice square waves.  The AND Gate can run the stepper motors.

If you will be using different speed PC's then your program cannot just use loops to do the work. You should try to put most of the work on the circuit board.

Perhaps a DOS boot disk might be better so that Windows does not mess with the program.

Ted