Now that i have the 5.3 to 6.0 swap done my motor is throwing codes.

It is throwing a MAF sensor code, Knock sensor code, and multiple cylinder misfire code. The motor seems to run fine, it just a tad bit rough at idle.

Is it throwing the codes because I have not had the PCM tuned for the 6.0 yet, or is this something that i should start to look into?

Also, is the proper spark plug gap for the 6.0 .060? I went by what the radiater cover said...