The BOB doesn't create the STEP/DIR signals. They are created by Mach3. All the BOB does is make them more accessible, and add some isolation, than you wiring directly to the parallel port plug. The relative timing of STEP and DIR signals should be configurable in Mach3.

You may need to experiment to see where you can pull out the signals. If the parallel port has the drive strength, you might want your step display board between the port and the BOB.

If you wish to inject your own signals, you must do it in such a way as to not drive signals backwards into the parallel port. For example, if the port is driving a signal low and you force it high, there may well be an incidence of magic smoke emission. Then you will emit some swear words, followed by an emission of money as you buy a replacement computer. Some logic gates would allow your extra signals to be combined with the parallel port signals, with the added bonus of giving stronger signals that your display could read.

So overall, the computer parallel port and your signal generator would feed into some sort of combiner or multiplexer, which would in turn feed both the BOB and your display module.

The signal combiner or multiplexer part is not immediately obvious. An OR gate seems like an obvious candidate but fails if, for example, Mach3 leaves a DIR pin HIGH when you wish to jog in the DIR pin LOW direction.