You want the harness off the 4.0 engine.
Assuming you have a donor '99 4.0, automatic, 4WD, and are installing into a truck with 3.0, automatic. Also, assuming you have keys for the 4.0.
Starting with the easiest and working our way along. The a to z of the swap.
a. remove lock cylinders from the doors from donor.
b. insert key into steering column barrel, push screwdriver (phillips or robertson) into hole in steering column and remove barrel - its twist and pull.
c. disconnect battery
d. disconnect alternator
e. open the glove box door completely and undo the passenger's airbag (couple nuts and wiring connector). Then undo the PATS module from behind the passengers airbag, again couple nuts add wiring connector.
f. undo the wiring connector from the PCM on the passenger's side of the engine bay, then undo and pull the PCM.
g. undo the wiring connector to the cab on the engine driver's side.
h. undo throttle/ cruise cables.
i. undo the front and rear driveshafts
j. depressure a/c and remove a/c condensor
k. pull the rad, I also like to remove the fan for more room.
l. disconnect starter
m. disconnect the fuel line
n. unclip the transmission shifter
o. undo the transmission lines.
p. unbolt the engine mounts.
q. unbolt the transmission mount and remove, disconnect transfer case shifter (wire if electric, shifter if manual)
r. unbolt the exhaust at catalytic converter outlet (this is usually grinder/sawzall operation for me, but sometimes I remember to take truck to muffler shop and get them to do it).
s. disconnect the power steering pump from engine brackets
t. check for anything still connected
u. check for anything still connected
v. check for anything still connected
w. pull engine, transmission and transfer case. (if you split the transmission from the transfer case, a couple liters of oil will pour out, and it will continue to pour out as your remove the engine.
x. repeat on existing 3.0 truck
y. reverse for re-install
z. sit back and enjoy beverage of choice, you've earned it.