I'm swapping a 3800 in right now and I'm in the same boat. From what I can determine from the schematics I've looked at, the larger black wire on the stud of the alternator and the PNK/BLK out of the connector are connected further down the line and then connected to the junction block near C500 by Fusible Link E which is the largest link there. The brown wire goes to the brown wire in C500 which goes through a diode and to the charge indicator light. According to my schematics, this diode is between C500 and the CIL, so no need to worry about it.
That said, I haven't hooked mine up yet and can't verify the accuracy. I looked at the Ogre's site just now and this seems to verify what I've found but cautions that all alternators are not the same. If I've read it right, he also says if you're not sure which alternator version you have to hook it up as above.
And to (finally) answer your question, I'm essentially connecting brown to brown and pink to red.