Truthfully a stock motor is going to have some knock. The U-bend and crappy intake is horrible for flow and add that with the low octane gas and you get what you get. I have heard some motors getting up to and over 6* of knock on a completely stock motor on 93 octane. New plugs, new filter might help a little but probably not much. You need to get rid of the u-bend to really get it down and bigger piping (headers/3" downpipe) help even more.
This is why we recommend headers/intake first then tune/pulley. Gotta have flow and knock down as low as possible before pushing more air in.