Restoring the original radio harness

Well, as I continue to undo the carnage the previous owner(s) did when installing an aftermarket stereo/amp, I've moved on to the actual head unit itself. There was an el cheapo Kenwood installed that would not power on (stuck in PROTECTED mode) so I've pulled that out and from looking at the miles of electrical tape used to splice in to the stock harness, it does not surprise me that there were electrical gremlins I've repaired the splices for constant power, switched power, and ground and they are good to go but I see a few things that seem a little off so hopefully someone can shed some light on if everything is back to its original configuration. This is a 2003 with Bose/MOST and originally had the CDR23 and no CD Changer so only the Black and Yellow plugs at the radio side. 1) My car did not come with a CD changer from the factory but I see the wiring harness and MOST connector underneath the panel where the CD changer would normally live. Was the CD changer pre-wired on a 2003 or did someone add that later? 2) On the Yellow plug, pin 4 for wakeup/diagnosis (white/red) splits and goes off in two directions. I traced it and it appears to run to both the CD changer harness and the original amp harness so that makes sense at a high level but the way it splits is very rough and does not appear how they would have done it at the factory. Maybe someone tried to tap in there for the aftermarket setup (no idea why) and this was their fix? Or per my question #1 above, this might have been someone's ham-fisted approach for wiring in the CD changer later... 3) On the Black plug, pin 5 (white) has a rubber "cap" a few inches from the plug. There aren't any wires coming from it and no signs that there ever were so not sure what this is or if something is missing. 4) Again on the CD changer, the MOST cable is there but it is open-ended. Does that need a loop bypass if I am not planning to have a CD changer installed? My understanding is that the full MOST loop would be one circle: Head Unit -> CD Changer -> Amp -> Head Unit so without the CD changer, I need something to bypass that node. 5) I'd like to pull the pins from the Black plug to slide some heat shrink over my repairs without actually cutting the wires. I removed the sliding yellow "lock" from the base of the plug but I still cannot get the pins out. Am I missing something? Still a ways to go but I feel like I am making progress in getting this back to stock.

I believe you do need a loop for the fiber optic. To get the pins out of the plug you need to remove the lock which you have already done. There there's a "catch" on the pin itself that need to be depressed to pull the pin out. Where the catch is depends on the pin. Some are on the side, some are adjacent to the part of the pin that makes the electrical contact.