If you really can't temp attach a CD drive as Dave Patrick suggested,
and must somehow get the CD's install directory into the machine via
DOS, there may be a couple of ways to do that depending on the machine's
hardware. First, though, you should check carefully that the embedded
machine actually meets W2k's requirements, including a fairly large hard
drive, and that W2k drivers are available for all the componentry you
wish to be able to use (including mainboard chipsets). W2k itself really
needs to reside in at least a 4GB partition if you'll have more than the
simplest applications. And the install directory (i386) contains 4000
files, 11 of which are >1MB. Of those 11, 3 are too big to fit on a
1.44floppy, and one of those - the file of drivers - is 51MB.
If the machine has a tape drive, or some sort of lan-like connectivity
to a standard PC, perhaps you can move that directory over that way. If
you have a very large hard drive, it would be a good idea to move all
the CD directories associated with an Intel-based install.
Your headaches may continue over the long haul, unless the embedded
machine has internet connectivity. The service pack files, if you plan
to use them, are also huge. SP4, the latest, is 132.3MB. The SPs are
available only on CD or by download.