If you boot from the USB drive, all you need do is run the sys command,
and give it the drive letter of the hd, then remove the usb thumb drive,
and the hd should boot just fine.
sys d:
should do it in your case.
you should also copy command.com to the target drive and
preferably write a config.sys and autoexec.bat there using
a text editor of your choice...
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