DaButcher,
You found a gem. A rig stored indoors all it's life and well cared for will be a gem. I am happy for you.
You do what you think is right. But as for me, I would not be quick to replace things due to age. Some things like cooling hoses and such, the one you buy might be just as old as the one installed by Ford back in 2001. Even your anti-freeze is still good because the rust inhibitors breaks down with heat, not age. And ethylene glycol never breaks down. I would change the motor oil & filter, the air filter, flush out the old brake fluid, inspect the belts for cracks, and leave the rest of the chassis alone. 13,000 miles is so little heat degradation.
What a wonderful find.