allthough it is possible that the diskfailure is by coincidence, it would be interesting to look at that tool, were the two disks Maxtor disks?
AND
Does your friend still use the program? have they had any problems?
Coincidence is the situation.. In your first post you said..
It ran fine for a couple months and one day while using it, my computer crashed bad.
I don't know why I missed it.. You were useing the prog for a couple of months..
How long did you Boss use the program before the HDD Failure?
A sudden failure of the HDD of any sort even a simple bad sector will "Crash Badly"your system..

While I am not ruling out Malware.. I place it a 95% Certainty that it is a coincedence for your situation.
An as the program was warez.. regardles if your friend d/l it or owned it outright.. once he passed it on to you It must have been a burnt CD.. meaning you had a pirated copy anyhow.. NOT ORIGINAL CD.. SUSPECT PIRATE COPY..
And your Boss he is also a pirate