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Hello and welcome to Just Answer!
It looks like you are looking for some advise on where to get what looks like alot of service work done.
Let me start by saying by 100,000 miles, pretty much every system on the vehicle should be serviced.
I would definitely recommend the tune up and differential fluid change. Also have the transfer case fluid changed as well. Transfer cases have a high failure rate on this vehicle and you need to do everything you can to prolong it's life. The transfer case is the part that connects the transmission to the front and rear axles for theXXXXX
As far as the pinion seal, without being able to see it myself, it's going to be hard to say if it really needs to be replaced. I would suggest having it changed when the differential fluid is changed because of the loss of fluid that will occur when the seal is removed. You won't loose all the fluid, but you will loose some so you might as well only by differential oil once.
You have 2 options as far as where to have this work done. Dealer or "not the dealer"
there are 2 things to consider when choosing where to have your vehicle serviced. Both places have their ups and downs. It really depends on what is most important to you.
first thing is price. The dealer will usually always be higher. How much higher depends and can very. Use your written estimates to compare the prices. If you don't have written estimates, GET WRITTEN ESTIMATES FROM BOTH SHOPS!!!! Never have any work done without a written estimate!!!
second thing is warranty. Dealerships will usually give you a 12 month 12,000 mile warranty on what they do. Most independant shops will have 12/12 warranties as well, but sometimes can be even more than that. the difference is that dealer warranties will be nationwide. You can have warranty work done at any Ford/Lincoln/mercury dealer anywhere in the USA. Some independant shops have nationwide warranties but they can be troublesome to deal with and are provided by third parties.
Basically you have to decided between saving money or getting a hassle free nationwide warranty. While getting your written estimates, make sure there is a warranty statement on the bottom of your estimate and if not, ask for a written copy of the warranty from both places.
Often times independant shops have nation wide warranties so you may be able to get the best of both worlds from the aftermarket shop.
I'm not sure you are able to properly use this chat mode so i am going to switch to Q and A mode.
thank you for the info. I'm now concerned with your mention of the transfer case. Does it pay me to keep the vehicle. Will the transfer case eventually die, even if I take care of it? It seems that you might prefer the dealer since I intend to keep the vehicle. I don't want to be penny wise and dollar folish but if the truck won't last anyway why waste the money.