I see this post is a few years old, but I'm curious how this turned out and I'll give my input anyway. This thread may be of use to others facing a similar situation in the future.
The best way to construct a trail is always to just blaze it in a fairly capable vehicle.
Mud holes will form themselves, and there should probably be a way around them for the guys with smaller tires. If there are no trees nearby to winch up to, then sink a pole in some concrete at each end. You'll need an engineer of some sort to determine what will exceed most stresses on it, but I'd think with decent soil compaction, 5 feet down and 2 feet around aught to do it. If you really want to choose a place for a mud hole, look for where water collects and run a plow through the thing to loosen up the dirt. Rocks are fine naturally, but small ones become projectiles that can damage paint and be a nuisance. Nothing large enough to cause any real injury will get stuck in a tire tread. Large wocks will only cause slippage. Any rocks will promote drainage and counter water retention required for mud to form and remain.
For rock crawling, same rule applies, see what you can drive up in a failry capable vehicle with an experienced rock crawler driver, then blaze a bypass for those who can't make it up. Place a sign at the bypass and maybe a rating for the obstacle from 1-10.
One of the best examples of a natural trail is the Rubicon from Georgetown CA to Lake Tahoe. That used to be a road, it was just an unmaintained road. The rocks and things that ended up on the trail were from purposed lack of maintenance, some abuse from drivers, mild erosion, and other natural forces. There is no reason to over think a trail and no one fusses about roads much.
We will gladly tear a swath through a landscape wide enough to accommodate 8 lanes and surrounding buildings for hundreds of miles, but God forbid we make a little trail through the woods and some guy spills a quart of oil on it.
Asking advice is always a good idea, especially for anyone who thinks they are too smart to do so. Hats off to the original poster for asking! Very best wishes on this project, even if it's now complete.
If anyone has anything to add, please do. I'm not above advice myself.