I have a 2006 Ford f150 4.2 I was told that the number three cylinder was misfiring I changed the injector but now it's a rough idle what could it be

 

Sounds like you still have a misfire. Check for codes. (P0303 would be set for a # 3 misfire) and let us know if there are any. If its worse now, maybe the new injector is bad or the o rings got damaged when installing the injector.