The guy at Crutchfiedl was NOT accurate with you. With ANY speaker, clipping comes from overdriving the amp...have you made any adjustments at the head unit, i. e., played with the limited bass/treble controls? You may have to cut back on the bass to reduce the distortion you're hearing. Sound is a waveform, and when you flatten the top of it (when looking at it with an oscilloscope, for example), that indicates that the signal is being cut or clipped...I'd be careful of replacing the stock amp if there is no need. There are a number of other things (automatic volume control, for example) that will be eliminated if you replace the stock amp.

I would suggest, if you have a speaker that only has the foam that has torn/separated, take a look at my thread on repairing it with tissue paper and rubber cement. I have done it to one of mine some time ago, and it's still working fine!