I'm trying to pinpoint what is making my vehicle shake. Can anyone be of assistance?

I have a 2004 Ford F-150 4.6 RWD truck. It shakes/vibrates when driving it. I just changed the front wheel hub assembly s including the rotors and brake pads. The tires are inflated to 35lbs per the vehicle door tag. I have had a alignment, tires rotated, spark plugs, and all COP changed to new ones. I still can't find why it does this.

Stop driving, if the shakin stops then you know it is because you are driving. So stop driving and you won't have this problem

Engine Mounts? Misfire codes?

Get the wheels balanced (if it was not done) and check for bent rims. Have a shop check the U-joints in the driveshaft and the driveshaft itself. Driveshaft might require balancing.

Could be any or all of the following.
Worn tie rod ends, control arm bushings, steering dampener, shocks, ball joints, or really bad universal joints on the drive shaft.
When you had the alignment done they didn't say anything about worn suspension parts? How strange.

Hm, just remembered a problem I had on a '72 Ford LTD wagon I had once. I bought it used and felt a vibration at highway speeds. Had a buddy drive along side me and he reported that the right rear wheel was bouncing like a basket ball. Pulled the rear wheels and found that the brake drums were mismatched. One was for a sedan, the other for the wagon with tow package. Installed the correct (matching weight) drum and that was the end of that.

Check the u-joints

Maybe a bead in the tire broke

If you repacked the wheel bearings (you should have) you probably did not torque the bearing retainer nuts correctly. If you didn't repack the bearings you could be trashing those bearings as we speak.