I have not had time to touch up the trim, but Ill post the pics from the running boards and step trim. I originally wrote down the tool used, but lost it after the knock on the head with the ratchet. I decided to remove the running boards because I was afraid of the over spray. I am sure you can leave them on and mask around it, though you might not get even spray in the back if you dont remove them.
Here is the original driver's side running board. It is bent up because I tried to remove it incorrectly. Underneath, there are about 16 nuts that hold on the plastic trim. Do NOT remove these. They screw on to plastic pins from the trim. These are very flimsy and easy to break.

This next picture shows how the running boards are put together. There is a metal support. This runs the length of the board. (solid black line) The plastic trim that sits on top of the support (dashed line). The bottom shows the brackets that mount it all to the car.

Here is a profile shot of how the running board is mounted. The bracket is attached to the car by a bolt and nuts. The bolt goes in through the top most holes, and the nut on the ledge just below it.

Some pictures might give you a better visual.
Looking at the running board from the side. You see the support here with the trim on top. (bent) You can also see the side of the bracket.

Here is the running board taken from behind it. You can see two nuts in the center. These screw into 2 bolts sticking out of the body. Following the bracket, you see it tucks in behind the E brake line. A bolt goes in here through a hole in the body of the truck.

Here is a shot of the entire side. It is easier to understand how it attaches to the truck. Ignore the tool in the photo.

To REMOVE:
You will need to notice that there are three brackets. Only the center bracket had two bolts in the top to unscrew. The other brackets had only one bolt. All three had 2 nuts each.
I removed the top bolt from each bracket first and immediately lost them. I then used a jack stand on one side of the running board to support it as I removed the two nuts. I removed the nuts from the center bracket and lost them as well. As you remove the nuts from the last bracket, hold the running board so it does not slam into you. You might be smarter than I and have an extra jack stand here to hold it.
To clean the boards before painting, I used Simple Green to remove any dirt and wash/wax that might have built up on it. We used 4 coats of textured non gloss black automotive paint. Though the running board is already textured, the additional grip is nice.

TO REINSTALL:
Follow the steps in reverse, trying not to slam the ratchet into your head. You have to angle the bracket so that it fits over the 2 bolts sticking from the body. I installed the nuts for each bracket first, then moved on to the bolts in the top. On the driver's side, I was unable to angle the last bracket around the emergency brake line. I had to remove the 4 bolts that attach the bracket to the support at the very bottom. Be VERY VERY careful if you have to do this as the bolts that stick through the support can easily pop through the hole and become lost in the channels under the plastic trim. This is where the foul words came into play. I had to remove the trim enough the slide a finger in and pop them back through.
If you are patient, you should be able to slide the bracket around the E brake line without removing the bracket. It also helps to have more than 8" of room to work with.
BUMPER TRIM:
To remove the bumper trim, there are three flat nuts that you have to remove from under the truck. They are at both ends and one in the center. You will have to use an extender to reach them.
After you remove the flat nuts, there are 7 plastic push pins you must remove from the back of the step. These are similar to the pins that hold your interior trim in place, but they have support trim that they expand into. Remove them from the center and pull out the pin, then the trim.
Push on the edge of the trim towards your truck. This will loosen the front hooks. Then pull the back trim towards you to release the rear hooks. ( I believe they were opposite, but be gentle so you dont break them)
EDIT: After looking at the pictures, It appears these are not hooks, but friction pins that should pop out in an upward motion.
Picture showing the rear push pins.
Close up showing the pins the flat nuts screw onto (plastic) and the hooks.
Final product of the rear step.

Reinstall is easy, just dont over tighten the nuts on the pin as they are plastic. I used 4 coats of the textured paint again.
Over all I was very happy with the outcome. The once gray trim is now a flat black. I will tackle the trim on the doors, hatch and the roof rack in two weeks as I will be working next weekend. All credit goes to parad1mg for the original walk through and you guys for reminding me to do it. And my father for helping me along.
Parad1mg's original thread on 2 gens.