I am not familiar with the particular machine you are talking about, but the mastercam software should be OK. It will convert the file into G code which is what a machine runs on, and, as far as I know, is common to most machines.
Unfortunately, however, I do not think Mach3 will run on Windows 98, so you will have to update your computer to Windows XP or Vista. The problem with that is, if you buy a new computer, it may not have the correct ports for connecting to your miller. Is there some interface card between the Compaq and the milling machine
How does the Compaq communicate with it ??