Originally Posted by TimFreeh

I'm confused.

In your first sentence above you indicated you were able to see 6 codes and erase 4 - this indicates at that time your scan tool was able to see/communicate with the N3/9 CDI main control unit. As I recall the glow-plug output stage error is from the CDI control unit?

However your screen shots in post #5, after you disassembled things to verify that the plug to the alternator was all good, indicates your scan tool can no longer see/communicate with the N3/9 control unit. So at this time you can't see any codes until you can get your scan tool back into communicating with N3/9.

If the car starts and runs you have power to the CDI control unit. If the CAN wiring to N3/9 is good your scan tool you should be able to communicate with N3/9. You have to get the communication working before you can really continue.

Given the LIN bus is apparently shared with the Glow plug output state and the alternator, and the error appeared immediately after alternator replacement, it seems kind of likely that the new alternator doesn't understand its supposed to communicate with a LIN bus and has done something to take down the bus.

As Jay-bob said in his post he and others have replaced alternators with NAPA sourced remans and had issues. I realize your Bosch alternator should be of higher quality but I'd bet there are a couple of different versions of that alternator that share the same basic case and maybe you didn't get the version that is LIN capable?

You need to figure out why your scan tool isn't able to communicate with N3/9 - I don't think that problem has anything to do with the new alternator or the LIN bus. If you can get N3/9 back into communication I'd disconnect the plug to the alternator, which would isolate that LIN bus connection, and see if that brought the LIN bus back on-line which should erase the Glow-plug output state error in the CDI control unit.