It's done!
Me again, just did the running board removal yesterday (with my husband's help of course). I have a 2000 EB 4x4 5.4L, each running board had 4 L-brackets, 14 bolts, and 1 electrical clip for the lights. One warning, don't take these off a late-model unless you plan on keeping them off, since several bolts will most likely break during the removal process from being rusted on. I started using a 13mm combo wrench and my husband went after with his impact gun on the ones that were stuck (should have used that from the beginning, would have taken 1/2 hr max!). Wear your safety glasses to keep dirt/rust from going in your eyes as the bolts are coming off. And yea either have someone there to help hold them as they're coming off or use blocks. They're not heavy but definitely bulky and grimy.
It looks so much better, like an instant lift, think F150 supercab/short-bed with a cap. I'll post some pics when I get a chance.
There was some minor rust on the surface that was between the running boards and the body, but mine was all underneath so you can't see it when looking at the car from the side. I think that's pretty good considering this car has been in DE all it's life which means 11 winters with at least a handful of road saltings each year. I plan on using a wire-brush then anti-rust paint to keep it from spreading.
If you're worried about rocks install mud flaps instead. That's not something I'm overly concerned about since it's already 11 years old and most of the time it's covered in mud down there anyway.
Also, I have 3 preschoolers but for me that's a reason to take the running boards OFF. They would hold dirt and/or water on the top, which would mean my kids would be smeared with it every time they used the running boards to get in or out. They need a little help getting in now, but at least they're clean for church on Sundays! I suppose tube-type side-steps would be better for that but no money for that now and I'm liking the look without...
Will post some pics soon!