So I installed SysPrep for windows XP and ran sysprep -clean to prep
my hard drive to be used with another motherboard.  I've since decided
not to do that and uninstalled SysPrep, but there are some prevailing
problems caused by installing SysPrep.  Firstly, everytime I startup
the computer, my Start Menu shortcuts are gone. It builds up as I run
programs, but I guess SysPrep clears it everytime I reboot.  Secondly,
new devices are no longer automatically detected and installed.  They
show up in device manager and I have to manually select update device
drivers.  So, how do I totally get rid of SysPrep and reinstate these
features? Thanks in advance.

Maybe you could try System Restore to return the PC to a previous restore point.
System Recovery program is a last resort to reinstall the operating
system and the application software.
I'm getting this from my "PC Troubleshooting and Maintenance Guide".