Shimmy, Shake

I've got a 2000 2WD supercab F-150 that's got a little shimmy problem that seems to be coming from the front end. I've experienced it for a while, but it's getting annoying. About 6 months ago I took the truck in for it's 100000 mile check-up and had a few things done to it and had it all checked out. When I got it back the mechanic told me that my tie-rod ends and balljoints were in terrible shape, dangerous was the word he used, and told me that I shouldn't travel very far without replacing them. They quoted me about 700 bucks to fix them, which I obviously turned down because I can do it myself for a lot less money, which I did and probably saved around $500. I figured, at the time, that would fix any vibration or loose feelings in the front-end, but it didn't. Here is exactly what I'm experiencing: vibration when accelerating or decelerating to 40 MPH (always becomes noticable at 40 and moreso when hitting the brakes). Above or below 40 and I can't feel anything until slowing to a stop. When coming to a stop the truck seems to lunge, almost like one of the rotors may be warped. I replaced the rotors a couple of years ago because they were rusted and pitted so bad they couldn't be turned and because I feel the shimmy when accelerating it leads me to think that it's not the rotors (although it could be). What I'm thinking is that maybe the wheel bearings in the front could be going, or gone. I didn't changed the bearings when I replaced the rotors or the ball-joints, I just repacked them. Am I hitting it, or is it just the rotors? Or something else all together? Thanks in advance!

I should also add that I checked the rotors when fiddling with the ball-joints and tie-rod ends to see if there was any noticable warp, which I couldn't find.

I think you have more than one problem, not surprising with many miles on the truck.
The 'lunging' when coming to stop could be a warped rotor or one with a bad spot in the casting, or maybe the wheel bearings need to be checked for being loose, i.e. not adjusted right. This is hard to check without freeing the rotor from the embrace of the pads. Try squeezing the caliper pistons back in 1/8th" and then check for wheel bearing 'play'.
The shimmy at 40-ish speeds is due to some imbalance or non-round condition of a front wheel or tire, probably made worse by lack of toe-in or other alignment change that is normal with miles and years. It could be a tire with some bad cords or a delaminating tread, or that has lost a balance weight. Try swapping tires from the back to see if the problem changes. It could also be a wheel not mounted flat to the hub, or a bent wheel. If your front suspension bushings are deteriorated (such as oil soaked) it would allow the shimmy to be more noticeable.
Getting the steering box adjusted would also help the shimmy, and help vague steering in general. I dont know about Fords steering boxes, but they are ALL adjustable, and should be adjusted about each 20,000 miles, or the truck wont steer as sweetly as it did when new. Both the steering shaft and the pitman shaft have adjustments, and both of them should be slightly 'pre-loaded', enough to eliminate any play, but not enough to cause noticeable binding when you are turning the steering wheel. It may be able to be done on the vehicle, with the usual limited access due to other stuff being in the way.
Good Luck

"both of them should be slightly 'pre-loaded', enough to eliminate any play"

I am not so sure that there should be no free play in the steeriung shasft.

Im fairly sure there should be no play. With a new steering box, that isnt installled in a car, the preloading would be enough that you would not be able to turn the steering shaft stub with your fingers or hand. You would be able to turn it with pliers though. This amount of pre-loading would amount to a couple of ounces of force at the rim of the steering wheel - but its hard to determine that small an amount when the steering box is in the car, connected to the steering components - pitman arm, lateral steering rods, etc.
When adjusting a steering box its important to loosen the pitman arm adjustment first, and snug up the steering shaft bearing adjustment, then to turn the pitman arm adjuster in just until there is no play, plus perhaps another 1/8th of a turn. Thats the typical procedure for Saginaw steering boxes on GM and mopar tructs, but I dont know about the Ford settings. They use different steering boxes I believe.

I'm guessing that needing to adjust the steering box would mean that the shimmy I'm feeling would be felt in the steering wheel. I'm actually not feeling it in the steering wheel much at all, nor am I feeling it in the brake pedal, just in the front of the truck as a whole. So that's kind of what makes me rule out the brake rotors or any of the steering components. The steering wheel doesn't have much play and is still quite responsive. The truck does have a lot of miles on it; over 100,000.