Right front tire

the 2.2 engine and the 4.3 engine with 2WD MODEL you have to remove engine.the 4WD MODELS, you have to remove all these parts first remove dip stick, drive belt, splash shield, remove front axle shield and the transfer case shield, front skid plate and the flywheel cover,remove left and right engine mount through bolts.then raise the engine using a lifting device, and block in position,using large wooden blocks between the motor mounts and brackets.you will also need to remove these parts,remove disconnect oil cooler line, remove pitman aem bolt and pitman arm, remove idler arm bolts and idler arm, remove front differential through bolts,remove front driveshaft if necessary,remove differential assembly by rolling it forward for clearance, remove starter motor, then remove oil pan bolts then remove oil pan, your oil pan need to be flushed slightly forward of rear of the block to allow proper alignment with the transmission housing.using feeler gauge measure the 3 oil pan to transmission contact points.clearance should not exceed 0.011 in. 0.3mm if so realign the oil pan.oil pan bolts torque is 18 ft lbs tighten oil pan bolts in sequence.

You could have a bad tie rod end, Idler arm, pitman arm, wheel bearing or ball joint. All of these will normally cause a vibration also. Check by jacking the front end one side at a time and moving the tire back and forth on front and back and in and out on top and bottom. Either watch or have someone else watch the steering assembly for movement and where it is. If there is no unusual movement, it is more than likely an alignment problem or tire problem.

You could have a worn idler arm and pitman arm. The idler arm is more common to wear out before the pitman arm so start with that and have the front end aligned. Inspect all your front end steering components for damaged and worn out parts that need to be replaced.
Thank you for using Fixya, you did replaced your brake rotor when you replaced the brake pads right???

The clunking noise can be from a control arm bushings which makes these noises

If you can absolutely verify that there are no loose components in the front end I would start looking at the tire for belt separation. This can be detected by rubbing your hand gently over the tread area. Feel for bumps,bulges, and irregularities. It should be fairly obvious.

You can also try putting the tire on a different location and see if the symptom moves to the new location.

You should consider looking into one of Strutmasters air suspension conversion kits. Here is a link to their Lincoln Navigator suspension: http://www.strutmasters.com/lincoln-navigator-suspension-s/39.htm

check tires for balance or defect

Let me see know at 45 miles per hour a vehicle usually shifts gears into the highest gear so could it be the torque converter hanging up and not shifting quick enough or maybe its the U joints. Have the transmission fluid checked for proper level and color.
Here's a small test for you when your accelerating up to 55 miles per hour try letting off the pedal at 44 miles per hour and then reaccelerating up to the 55 mph and tell me if it`s smoother if it is then chances are that it`s hang up on third gear. There's also a electric sensor located on transmission that assist shifting it`s usually controlled by the engine timing.
One more thing did the repair man check to see if the tires where directional tires if there not put on right it could cause vibration and early wear out .Hope i helped you.

tire pressure low,alignment jack up the front end and wobble the tires side to side the body lift would not effect this

This is Caused by an Out of alignment Front end. Get the Front end Alligned and your Problem should go away.