I don't have all the answers, but know of one reason how cracked manifolds can produce KR.
As you know, KR stands for knock retard, which is your PCM retarding the timing when it "hears" knocking/pinging that indicates spark knock. Sometimes a knock sensor will react to sounds other than those produced by detonation. A noisy mechanical fuel pump, a bad water pump or alternator bearing, or a loose rod bearing can all produce vibrations that can trick a knock sensor into retarding timing.
You may know that cracked manifolds will make pinging sounds that produce sound waves that the knock sensor "hears" as spark knock.
Mike: 1997 SE w/ 183K, aka White Horse
, Gutted Airbox w/K&N, drilled 180* t-stat, tint all around, clear corners w/SilverStars, "PONTIAC" light up tail, PEMs, NGK TR55s