Hello Charles,
to clone OS/2 or eCS is pretty simple: 'xcopy x: y: /s /e /h /t /r /v' is enough to copy the system. As far as I remember afterwords you have to run 'sysinst y:' to make the new partition bootable. In the example 'x:' is the source, 'y:' the target.
The drive letter of the boot drive and other drives necessary in config.sys sure have to be the same in the source and the target system.
And now the buts ...
If the hardware is all the same this procedure will work well. If it is much different - old system as source, modern system as target - it will probably fail or produce much problems. To add one or more drivers to the old installation in the new system is no big deal. To change from a single core system with no acpi.psd running to a new multi core system with acpi will be a lot of work.
With my best wishes
Hans v. Mangoldt.
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