what is the process that is taking the most CPU time during the slow down?
when was last time you scanned for viruses/etc?
I mean mouse/program being slow could have to do with program itself and not the hardware. I've had flash plug in crash chrome several times on a brand new machine, where firefox had no problems there. It's just that chrome has shitty plug in handling. So, if it all comes down to iTunes, try looking for an alternative, after all iTunes was written for Mac OS not windows.