Any special tools required? Just want to make sure I have everything before I get started.
A transmission jack would be very helpful since it will make it easier to get the transmission lined up so you can remove and (especially) replace it. If the transmission angle is off in the slightest the transmission will bind coming off or going on and you'll think you left a bolt on or there's a problem.
You'll need an E-12 extended torx socket to remove the upper bolt holding the transmission to the engine. Plus a whole bunch of extensions to be able to reach that bolt. If you want to remove the transfer case, you'll need an E-10.
Your clutch kit should come with a pilot shaft to align the clutch disk while bolting the pressure plate in place. A torque wrench should be used to tighten the pressure plate bolts to 37 ft-lbs.
Very lightly lube the shaft and clutch disk splines with grease, don't overdo it as you don't want grease slinging out onto the clutch disk and flywheel. Lightly grease the fork pivot and release fork pivot surface
If there's any glazing on the surface of the flywheel, just sand it off with a very mild grade of sandpaper or emery cloth. Do NOT have the flywheel machined or resurfaced, that is per the factory service manual. The reason being is it has a slight dome shape on the surface for smoother clutch engagement/disengagement. Machining/resurfacing it would remove that dome shape.
Place some high-speed bearing grease on your fingertip and grease the pilot bearing on the flywheel.
Finally, there's no need to replace the flywheel unless it is physically damaged. If you bought one, you can return it for a refund. RARELY are the flywheels damaged.
Good luck with it.