Help identification for tranny swap (Pics)

[tak-]

(images may or may not load, the host is a shithole)

I am in the process of swapping my '89 Automatic tranny to a '91 5Spd.

When I removed the auto tranny, I was left with these wires / sensors:




The last two, "C" and "D" came out the following holes. The wires for "C" were cut, because there was no way to disconnect or detach them.



I have asked some people, and most have said that the DOHC tranny has 1 more sensor (4th gear). From looking at the automatic transmission(above) and comparing them to the 5 speed(below) I am a bit confused. I have alot more wires on the 5 speed.

Can someone please help me identify what each of these are.
#1
#2
#3
#4
#5
And a shot of the whole thing:


If you can help shed some light on this situation it would be greatly appreciated. I need to know what the automatic sensors are, and what the manual ones are. What ones I dont need to use, and what ones I do.

And what is that orange tube?