OK, I'll try to walk you through it.
You're going be mounting the doors, and running the wiring harness from each door up through the fenders (from your original description, I'm assuming that you unplugged the door harnesses from the donor, and thus have about 4 feet of harness coming out of each door).
Once you have the two harness in the front corners of the engine compartment, you basically will be adding new wires to fill the gap between the two harnesses, and making the following wiring connections. Note that there are a couple of wire color differences, depending on whether the doors are 1991 or 1992 units.
And, I'm assuming that you'll be cutting the connectors off the end of the door harnesses, and just splicing your wires wire-to-wire. If you can get the mating connectors, it would better, but direct-splicing will work.
#1- Reconnecting two wires for the passenger window motor-
Tan/L Blue to Tan/L Blue; and White/Yellow to White/Yellow (1991)
OR
Yellow/Black to Yellow/Black; and Red/Black to Red/Black (1992)
#2- Reconnecting the two doorlock switch wires-
Pink/Yellow to Pink/Yellow; and Pink/L Green to Pink/L Green
#3- Reconnecting the two doorlock motor wires-
Pink/Black to Pink/Black; and Pink/Orange to Pink/Orange
#4- Connect the ground wires coming out of the driver side door harness to ground. You can crimp them into a ring terminal and screw it to the inner fender if you'd like. There should be two Black wires, one for windows and one for locks. Ground both.
There aren't any ground wires on the passenger side door harness.
#5- Window power-
There should be a L Blue/Black wire on both sides. These two wires need to be connected together, and then continued on to switched power. The original power source on the '88 for power windows was a 20A circuit breaker at position 14 in the fuse box behind the driver's dash. Even on a non-power truck, position 14 should have one set of contacts (the hot side). Run your extended L Blue/Black wire into cab, connect it to an inline fuse holder with a 20A fuse, then crimp a spade terminal on the remaining fuse holder end, and plug the spade into these contacts.
#6- Locks power-
On both sides there should be a Black/White wire. Same drill as window power- these two wires need connecting to each other, and then an added length of wire to go to the power source. On this one, you have choice, since locks need contant power (not switched). You can either run the wire into the cab with your windows power lead, and find a constant power source; or, you can pull power from the battery wire at the starter relay (which is how the factory locks are powered). Just be sure to use a fuse holder, with a 20A fuse.
That might look like a lot of work and wiring, but it's really not that difficult or complicated.
This older post might help you, although it's for '92 doors onto an '89 Ranger:
http://www.therangerstation.com/forums/showthread.php?t=12424
I'm sorry, but I didn't save an original file of the drawing. Otherwise I could have just sketched in the details for your '88 connections. The drawing was done for the power conversion on an '89, and there are differences in the power connection points.
Good luck, man.
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