Okay, now we can make some headway.
In the transmission harness:
BLK/WHT is a common wire for the neutral sensor, it should hook to common from the clutch switch assembly, and TPS and MAP and others (which should be blk/wht on the engine harness), and eventually to pin 46 of the EEC.
WHT/BLK is the other side of the neutral sensor and clutch switch, it tells the EEC when the transmission is disengaged. You're correct, it should go to the pink wire of the engine harness (which eventually hooks to a brown wire and then pin 30 of the EEC).
BLK/PNK is the return signal from the backup switch in the transmission, it should hook to blk/pnk of the engine harness, which goes to the reverse lamps.
PPL/ORG is the power supply to the backup switch in the transmission, it should hook up to ppl/org in the engine harness.
In the engine harness, the 3-wire set:
PPL/YEL Can't find one of these in the diagrams, so I'm going to guess. If it runs to pin 52 or 53 on the ECC, then it controlled one of the electronic shift solenoids in the AT. You won't use it with the MT, so insulate it well so it can't ground to anything, and secure it so it's not flopping around.
ORG/YEL goes to the VSS, at the back of the transfer case. Also make sure that the dk grn/wht wire from the VSS is hooked up to the same wire in the engine harness somewhere, and runs to pin 3 on the ECC.
RED I'm pretty sure this is to send power to the electronic shift solenoids that were in the AT. You won't use it with the MT, so insulate it well so it can't ground to anything, and secure it so it's not flopping around.
In the engine harness, the 5-wire set:
RED/WHT Can't find one of these in the diagrams, so I'm going to guess. If it runs to pin 52 or 53 on the ECC, then it controlled one of the electronic shift solenoids in the AT. You won't use it with the MT, so insulate it well so it can't ground to anything, and secure it so it's not flopping around.
PPL/ORG connects to ppl/org in the transmission harness, see above.
RED/LT BLU is the wire that goes to the starter relay, and had to go through the AT shifter before so that you could only start the truck in P and N. Now, I'm pretty sure you should just jumper it to the pink wire next to it (along with the wht/blk wire above).
BLK/PNK connects to blk/pnk in the transmission harness, see above.
PNK connects to wht/blk in the transmission harness, see above.
Note that the clutch triple-function switch is pretty complicated, and it appears there may be 3 different pink wires serving similar but possibly unconnected purposes there. If you can't get it to start when you step on the clutch, we'll dive further into that wiring.
Finally, the only remaining thing I'm concerned about is the other wire from the VSS (labeled dk grn/wht on my diagrams), which needs to run to pin 3 on the ECC.
You may have to look at the wire colors at the ECC to make certain of some of my guesses. If you see one of those wires running to a different pin than I mentioned, let me know.