Hello,
You can not use mach to pulse serial pins, you'll have to use the printer port, or any of the other supported ways (ncpod,Grex,Gallil).
If you want to use mach you probably should lock out 'system controls', en connect the drives directly (or better via a breakout board) to the printer port.
On the other hand, if your machine does what it has to do for you, why change anything?
Maybe the serial port is used to send G-code-files to your machine. In that case, you can use mach or better lazycam, to generate your G-code and use hyperterminal
to send tje files.
Hope this gets you (or your machine) moving!
Greetz,
Kris.