I replaced my stock lift pump last month after nearly stranding me on the freeway. I replaced it with an Airdog FP-100 and it runs great. The only thing I am noticing now is a knock or rattle aroung 1000 to 1500 rpm. But never while accelerating or under load. Could the lift pump failure have caused damage to the CP3?

 

I doubt it damaged the CP3. Wintertime is notorious for letting carbon build up on the injectors. Sounds like you are hearing a little bit of timing ratte. Another culprit would be the winter fuel. As soon as it gets warm enough hook up to a heavy load and go for a pull. Heating up the engine and burning the carbon off the injector tips does better than any fuel additive I have used, and it's cheap.