4.3 to 5.3 swap but now cant get alternator to charge HELP!

Ok, first off I am new to this site but love what I have read so far! My problem is I swaped my 2001 4.3l silverado engine out for a 5.3l from a 2000 silverado. The swap went well, The truck starts and runs fine except for one issue, the alternator will not charge the system. Put on a new alt. and still no luck, Ohmed the brown wire from the alt. back to the pcm pin(#15) And the wire checks out to be good(100% saturation), also used a ground light at both ends of the fuse link and have current at each end. The messege center displays the red battery icon that comes on and goes will the truck is runnig. Completely lost on what to check next, Any help would be greatly appreciated!!

This is going to sound dumb, but have you manually checked to see if it is charging? Or just going off the light? The battery light is a common issue with the swap it seems. If it is charging and the lights still on, it can be shut off in the tune.

Ok finally got the sytem to acutally charge I feel so stupid the issue was so simple, I had all the brackets powdercoated on the engine and the powdercoating on the alt. bracket was keeping the alt. from grounding on the engine block. Took the bracket off and ground the paint off the bracket around the 5 or six blots that hold the bracket on a now I can drive my truck the charging sytem is back working. I feel so stupid! As for the battery light it is still going on and off and I am getting a code for secondary air injection which I dont have on the motor, must be something in the computer also Trying to get a hold of nelson performance to talk with them about the tune havent had luck yet but will continue to try.

I have a 2001 sierra with the V6 I bought all the service manuals I have carefully read all the diagrams the battery light is due to the fact that the 4.3 uses a 2 wire alternator and the V8's usually use a one wire the truck does not like it so it turns on the light just read the diagrams and run the extra wire, it is basicly a dumby wire that checks for charging, both plugs are the same or use the 4.3 plug!