I installed an LC header and K&N intake. Sometimes the motor runs really rough and sluggish. Are there some tuning issues I should be thinking about? Or do I need to hook up a scanner and clear codes?? I'm not sure what is causing the problem but before the mods I never had this issue. Please help!

 

Should not need any tuning, might be a problem with the O2 sensor if you are using an aftermarket one that is too short on the sensing tip. Read the codes, it is trivial to do:
- http://www.4crawler.com/4x4/CheapTri...CheckConnector

with this "code scan tool":

 

Pull codes and reset computer.

 

Ok. I tried to pull the codes but when I used the scan tool the CEL stayed on and did not flash any codes. I went ahead and reset the computer but still same isssues.