Eh, it happens lol.
Welcome to the 3800 weirdness. Some cars won't knock, others will.
You may have reduced part of the restriction but you can't change the timing and commanded AFR fuel ratio doing what you did. The 104's are overkill for a stock pulley/downpipe combo. The thermostat will mean nothing, it won't help or hurt anything changing it.
On some engines the fueling is too rich, causing knock. Stock calibrations run 10.7-11.0 AFR with ease, which could cause some knock if it's too much. Or the timing needs to be backed off a degree or two to stop the knock. It's a game to play if you had a tuner. You could try 11.5-11.7 AFR, using a wideband to hit that target and or taking away timing or adding timing to see what changes.
Possible that when warmer temps come around that the knock lessens because the air charge won't be as cool thus creating less boost.
