Thanks for all the great input everyone! I'm surprised at all the responses I already got and will do my best to address all of them. Based on all of your input and the input from the Ford truck forums, I'm pretty sure I'll eliminate the PTO provision since it'll likely never get turned into a full-blown work truck. I think I'll keep all the other option boxes checked, and will give the moon roof some more thought over the next day or two.
I spent a long time debating on the long bed. With my garage limitations, I had the choice of an extended cab long or short bed or a crew cab short bed. Since I personally prefer the looks of the short bed and know the back seat in the extended cabs on the new trucks have less room than mine, I decided to go crew, short. The added advantage is I can fit a Titan 50 gallon tank underneath it and get to option the heated rear seats. I don't see a 5th Wheel in my near future and my current trailer is already a tough squeeze in the places we like to camp, so I don't have the need to go to a dually or F-450. They're awesome trucks, but driving and parallel parking a beast like that in a metro area would be a nightmare and there would be no offroading, which this truck will see quite a bit of.
The truck will have the 3.55 rear end as well as remote start (which is included with the Lariat Interior or Ultimate package). I'm feeling pretty comfortable on the price I negotiated for a 2016 special order based on more research and feedback from the Ford forums. It's about $1,500 below invoice and beats X-Plan by about $1,800. If the rebates improve, I'll save that much more. I probably could have knocked another $1,000 off with a lot more legwork and haggling, but it wasn't worth the headache. I envy those that are able to get $10K off sticker on these new trucks but I have never seen one go that cheap in our neck of the woods, especially on a new model year and a factory order.
Thanks again everyone! Now the long wait begins...