Shoe creek and flagpole are pretty stock friendly as far as mods to the truck. The main trails are fairly easy, with the harder stuff off to the sides which you can bypass.
As far as mud, there are a few creeks that i remember crossing at both places, but not a lot of mud. Mostly its just trails and obstacles. I guess if you go after a good rain there might be some muddy spots off the main trails but I think that kind of stuff is pretty discouraged since they are public trails and people don't want to see them get messed up.
Unfortunately where we live there isn't much for off road action that is LE friendly. I wish there was