Your automatic transmission cross member will work if you make the transmission mount holes elongated. I would grab the manual transmission cross member, they are the same for both years.
You will need the PCM for a '99 with the same engine that you have, but for a manual transmission; 4wd and 2wd PCM's are the same. You can have your PCM reflashed at a dealership, but that usually cost quite a bit.
Be prepared to spend 8-12 hours doing the swap. It is fairly easy and straight forward, but there are some things that could hold you up (stuck bolts for instance).
Get the manual transmission wiring harness. It unplugs at the top rear of the engine. Replace yours with the harness so you have all the plugs correct and don't have to jim-wack with wiring.
Make sure to install the CPP (Clutch Pedal Position) sensor. This again, will eliminate jim-wacked wiring making it all be factory.
Grab the steering column trim off the manual transmission truck. You can remove a pin and wire from your automatic shifter and it will come off your column. Then replace the automatic column trim with the manual column trim and you will never know it wasn't supposed to be like that. The good thing about the auto column with a manual transmission is that you don't have the pesky button to push to turn the key all the way back.
Get the proper floor plate from the manual transmission truck. This will make it much nicer during and after the install. There are 4-6 bolts that hold it to the floor. You don't have to remove the carpet to install it, just the passenger seat and the carpet trim. Pull the carpet up and go up under the carpet.
Anymore questions, just ask. I have done this swap about 4 times now.