MacBook Pro - Brand New MacBook Pro-Old Problems Transferred?

Advice needed: I admit to using Limewire and Frostwire in the past on a previous MacBook (purchased in Sept. 08). After a few months, I noticed that my energy saver settings were NOT being followed. In short, my computer would NEVER bring up the screen saver, put the desktop to sleep, etc. on its own - AND my hot corner settings to activate the SS or put the desktop to sleep wouldn't work either (it would last 3 seconds, then return to the regular screen).

Took it into the Apple store and spoke with a 'genius', who said that whenever he sees really weird things going on (like my problem) it was undoubtedly due to downloading files. He recommended I re-install my operating system (which I did) but the problem persisted.

I bought a brand new MacBook Pro on Monday, transferred all of my previous files, and of course now the EXACT SAME old problem persists on the new computer (now I know that the files are completely corrupted).

Obviously, I deserve this for downloading files, but here are my questions:

1) If I removed all of the files in question that may be affecting the problem (using secure empty trash) could this possibly rectify the issue?

2) And if I deleted everything, but kept the corrupted files on an external, guesses on whether it would harm the hard drive that I've just 'cleaned' when I play the files via the external?

3) MOST IMPORTANTLY - is my brand new hard-drive corrupted in some way forever no matter what steps I take to solve this?

Any suggestions would be appreciated. Thanks in advance for your help.