and also knock is the fuel/air mixture igniting too early?

Um.... then clean it out?

That's one cause of a knock... Definitely, knock is whenever a rod bearing comes into contact with the crank. This can occur from the fuel ignition too early (a couple causes for this: preignition or autoignition, poor spark timing, detonation can contribute, excessive heat) or from the fluid bearing failing allowing the metal to come into contact from the loss of hydromatic pressure.

if the egr was eliminated would the intake not stay clean?

No, not really. The PCV system is the primary contributor to any sort of detritus in the intake... if it bothers you add a catch can... we've already covered the reasons not to remove the EGR, if you still absolutely must find a reason to justify doing so then forget the justification and just remove it. But as for the dirt thing... it took 20 years for whatever carbon you're seeing to accumulate from the EGR system. Clean all the EGR passages out thoroughly and worry about it again in 15 years.