Burnt some Spaghetti!
So here's what I get when comparing the circuits in the FSM to your diagram.
Some have a slightly different color combination, but not enough to consider it a priority to figure out right now.
Overall the wiring on your car seems to match the diagram. So lets go through the ones that are trouble.
Position
B: B1-18 Bk. B is Back Up lamp circuit. (from page 6 of the Master Tech booklet,
324.pdf)
Big clue!
Position E: V3-Br. V is Wiper and washer circuits. Being in a different cavity may simply be due to a 2 speed rather than a 3 speed wiper or something like that.
Position L: S2-18Y. S is Starter circuit. More precisely this is the wire from the start position on the key switch to the starter relay. Someone has replaced this. Hopefully they just used a heavy wire because it was handy. However they may have converted to a off starter solenoid which the key switch can not handle.
Position
6: D6-18BK/LGN*. D circuit covers emergency stop lamp and turn signal circuits. We'll have to figure out specifically what D6 does.
Positions W & Z: Your car did not come with A/C so that's probably why the C2 and C5 wires are missing.