The '93 rear axles is stronger than the '96 Runner, so you should retain it, the locking diff from the Runner will fit in the truck axles with a little modification to the housing.

The wiring issue is a lot easier to do today than it was when the article was written, ORS supplies them now.
http://www.offroadsolutions.com/products/ors-3-4l-conversion-harness-for-3vz-e-and-22r-e-vehicles/

More than tread lightly. Leave it like you were never there, nor anyone else.
'90 X-cab 4.88's 33 BFG AT's, rr ARB, Headers, Ignition upgrade, cold air induction.
'91 X-cab 5.29's 315's BFG MT's, rr ARB, custom bumper and flatbed