Me and a friend changed out the alternator out on his car yesterday. now its misfiring and when we disconnect the battery the idle changes but the misfire doesn't stop. It also does the same thing when the alternator gets disconnected. Its misfiring on cyl 1&2 its getting spark but im guessing its not stong enough. Any ideas what it could be?

 

Pull out the DMM and check how much voltage the alternator is putting out.