Hi, Cameronian,
from all your descriptions, it's sounding to me like you have a rather old and commensurately underpowered computer running too many modern programs.
What's the RAM and CPU of this beast?
Therein may be the problem. Nothing should take that long. BTW, that program from Mesichdotcom is simply a modification to the standard '98 defrag, to turn it into the ME defrag. A bit like putting a mini cooper camshaft into a Morris Minor.