All good suggestions so far. The Red Rocks web site is a good place to search for trail descriptions. Charlie Wells book is good, but get a data card for your GPS from Funtreks as well. Invaluable technology. You cannot get lost with his routes superimposed on your (Garmin) GPS.
But don't go just by degree of difficulty. Moab is a place of tremendous beauty and the scenery can be spectacular on some of the easy trails. That said, here is a list of "must do" trails, not in any order.
1. poison spider / golden spike / gold bar rim. Listed together because you have to do poison spider to get to golden spike and then gold bar rim gets you back to civilization. Usually takes 10 to 12 hours. Can be done in much less, but you have to haul some serious ass.
2. Hells Revenge. Personally I hate this trail, only because I have done it wayyyyy too many times. But its a must do, signature trail. Find a spotter who TRULY knows the line up Hells Gate and do it. Its a special feeling. Too many people think they know the line, but they don't.
3. Metal Masher. Drive up to the Widow Maker obstacle just to check it out.
4. Steel Bender. One of my favorite trails.
5. Elephant Hill. Make sure you do the short hike to the slot canyon known as "The Joint". I promise you will be amazed.
Make sure you do those 5. The rest, well, fill in as you want. I like Dome Plateau for the scenery on the optional route to the cliff. And the cave is pretty cool as well.
Keep in mind that Moab can be pretty deserted in the fall, which is odd because it is a great time of the year to be there. Warm days, cool nights. I have wheeled entire trails without seeing another vehicle.
Colorado. You have to do Ouray. Black Bear, Engineer Pass, Imogene Pass, Poughkeepsie gulch, are all must do. Hurricane and Corkscrew pass are nice too. Up in the central part of the state, Red Cone is a must, must do. Red Cone to Radical Hill to St John's is a great full day trip. Spring Creek near Idaho Springs will test your rock crawling abilities. Chinaman's near Buena Vista is a great trail. And you have to stop at the exit to Carnage Canyon and walk down to see it. Just looking at the trail is enough to make the sheet metal bend on your jeep. Holy Cross, Iron Chest, are great trails as well.
Timing. When you say "fall of 2016", that could mean early September into late November. For the CO trails, you best be here before the later half of September. I have video of my jeep covered in snow coming down Red Cone in September. Its the same for the Ouray area as well.
For Moab, its still damn hot in September. October is much better for Moab. So do CO in September and Moab in October - perfect.
If spring of 2017, just cross CO off your list. Except for Chinaman, (which is open most of the year, weather permitting) everything else is closed until early July due to snow. Maybe late June, but don't make bank on it. Moab is great in the spring, but it can snow on you there too.
I have been taking groups to Moab for wheeling for several years. I know all the housing options, every restaurant in town, and just about every trail. I know CO very well too. If you need some help planning this trip, PM me. I am glad to help you organize a plan.