(Battery Light) 411 PCM Swap

[HybridLS]

Alright before i begin im new to the forums, an still need time to get familiar with the workens. I have how ever searched an been directed here several times for answers from google, regarding my 5.3 vortec. So i figured what better to do than create my own profile an join the club. Okay soo i recently done a #411 pcm swap, an had a friend program it with hptuners software. He is one heck of a mechanic, dialed it in while i was out of town with only 5 cylinders firing! (3 bad 01+ injectors). Long story short i got back replaced the bad injectors an it runs amazing programed for 93. The promblem now is the battery light flashes non stop in the service center. I read before in a diff forum somone mentioned they may have added an extra wire for the alternator after 2000. So im clueless as to what to do. Has anyone ever done this swap on a 99-00. If so what was your solution to the madness.