For those that have been following my problem trying to troubleshoot the check battery/generator message I have been getting on my 2006 911S with a 2008 911S engine, I seem to have solved the problem. I had checked Porsche schematics for the engine wiring harness for both engines, as I had read that Porsche had moved the blue alternator wire to go to a different DME pin between MYs 2005/6 and 2007/8. I suspected that possibly that was the cause of the problem making me get the warning message and P0621 DME code. After studying the wiring on both engines, I found that no signals wires were changed on the actual engine wiring harness, but the alternator pin was changed at the DME from the DME B connector to the DME C connector. So if the DME wiring harness was changed as well as the engine wiring harness and the DME harness from the engine wiring harness when installing the 2008 engine, then the alternator lamp circuit signal blue wire, would end up on the wrong pin of the DME which has no function on the 2005/6 DME. If the DME harness was not changed to a 2007/8 harness, but the engine harness was changed to a 2007/8 one with the engine, then the alternator lamp circuit signal will still be on the correct DME connector/pin.
I was able to confirm in my case that this blue wire from the alternator did have continuity to the correct wire on the engine wiring harness TSX59_2 connector's blue wire not TSX59_1's blue wire which I thought was the other end after unplugging the it and checking with my DVOM. So I put it back together, and planned to measure the voltage on that wire at the #2 engine harness connector tomorrow, but knew it will measure correct. I started up the car, and ran it a bit, and to my amazement, the warning message was gone and did not even show up in the OBC info messages history anymore! I think that the 25 pin engine harness connector was loose and plugging it back in and tightening it real well made it connect again, carrying the alternator lamp voltage to the DME!
I had replaced the alternator's voltage regulator thinking that was the problem, but that did not solve the problem. I have to recommend the OEM Porsche repair documentation from www.alldatadiy.com I purchased which included electrical schematics to help with me figuring out if I had a wiring problem from the engine change or from some other cause. I was not able to find these schematics from any other sources on the Internet and from other Porsche manuals. Yeah!
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Porsche 911 Carrera Alternator Replacement - 996 (1998-2005) - 997 (2005-2012) - Pelican Parts Technical Article