I did this to a 06, it was very involved...but I'd do it again. And from the looks of your signature I'd have to guess your not scared to do it.
I used the RKE/Security module, and harness from the donor that was also an 06. The donor truck was badly wrecked and the junk yard had cut the cab up so I had to splice the harnesses together. In places where the XL had the same existing wires I used them and spliced them into the larger "XLT" harness. So the door speakers, dome lights, brake light, door ajar sensors, seat belt restraint sensors etc I left intact and spliced in the new harness.
So its hard to explain, so forgive me if this doesn't come out correctly. Remove the seats and vinyl/carpet floor. Remove the seat belts(be sure to lock them with something like a close-pin so they do not retract all the way in) then remove the associated panels the seat belts/re-tractors are in. Also remove all the door panels. The door harnesses run down the drivers kick panel turns and goes across the cab floor behind the drivers and pass front seats. If its a crewcab the rear door wiring(windows & locks)for the drivers side rear door, speaker, rear dome light, cargo light, brake lights, continues down the drivers side bottom panel. If you can envision a "H" in the wiring layout of the cab if you looked down on the harness from above with the top of the cab removed. The other side does the same. But the harness originates from the drivers side of the truck and is plugged into the back of the fuse box. On mine I just unplugged the existing harness and plugged in the new one into the fuse box. I did not remove the dash, I was able to install the RKE/Security module from behind the radio.
This "H" layout of the harness is one huge harness, it does not break or have a connector anywhere in it. So you have to remove and unplug them in the doors and fish it out of the door and into dash and then out of the dash. Its sucks. I spliced everything back together with heat-shrink tubing and solder.
It went really smooth, the only hang up I had was when I was all done nothing would work. In that large harness on a 06 there a 12ga Orange/pk wire that is not shown anywhere in the ford diagrams. And in all Ford diagrams black is ground...except for the odd ball orange wire....its a ground too. It grounds to the truck cab up behind the parking brake pedal assembly. It works good now though. I didn't pay enough attention to it in my removal procedure.
I know that's not a very good write up, considering you doing a 99. To be safe I'd swap the GEMs if you have both of them...just incase.
If you need help PM me, I'll do what I can. I can scan and send some ford diagrams for your 99 if you need them.