From the page you linked...
3. The W2K Pro disks are zipped images from the MS CD. Best bet is to download them, upzip them to a new folder where you also put makeboot.exe and makebt32.exe into and then run one of the makeboot utils depending on if you’re in dos or windows to create the diskset. Or, one can use Winimage to just create a single bootdisk.
Did you try simply double-clicking makebt32.exe?
The question seems to be largely about the makeboots. How are they ‘run?’ Selected either of the two just makes a black screen pop up for a second, maybe less. Dragging the IMG files of the disks doesn’t seem to do much either. So how is the diskset made with either of the utils (guessing that those are makeboot.exe and makebt32.exe); how to get those to work?