With both front wheels off the ground, the front wheels should turn smoothly and easily. What you are describing sounds like dragging brakes and or bearing issues. If you have the pads off and the wheel still has trouble spinning, it is likely in the bearings if the CVs look ok.
The dust cap is looking like that because someone used pliers to remove the cap. I generally use a flat blade screwdriver or cold chisel to pop them off by putting the blade between the cap and hub and tapping lightly with a hammer to pop the cap off.
From your statement about the pulsation and the pictures, I suggest replacing the rotors. While you have the hubs off, clean them out and clean and inspect the bearings for wear or damage. If questionable at all, replace the bearings and races, they are relatively inexpensive. Replace the grease seal with a new one regardless. When I repack the bearings, I also fill the void in the hub with new grease, level with the inner bearing races. Grease is cheap and having the hub full like that helps keep the bearings happy.
The uneven wear on the pads is the result of several problems. One, the rotor surfaces are not flat and smooth. Second, you have worn abutment shims that go between the pads and the caliper torque member. Third, the caliper slides are not letting the caliper move smoothly. Pull them out, clean out the bores and clean and inspect the pins for wear and putting. If worn or have putting, good idea to replace them. It is also a good idea to replace the rubber hardware at this time.
When pushing the caliper pistons back into the caliper, I like to open the bleeder valve a bit with a 1/4(6mm) hose on the end going into a bottle to catch the fluid pushed out. 2 reasons for this. First, it makes pushing the pistons home much easier. Second, when you see what comes out, you will understand why it is recommended to flush the brake hydraulics every couple of years.
When lubing the caliper slides, us a good silicone based grease, petroleum grease will damage the rubber parts causing problems. For the metal on metal lube for the pads themselves, I use a molybdenum brake grease. A small amount on the pads where they contact the torque member and a thin layer between the back and the shims unless the shims have adhesive, then a thin coat between the pad and the caliper helps a lot with noise control. I also wire brush and was the caliper and torque member before lube and assembly. The cleaner it is, the easier it is to reassemble and the better the brakes work.
I do this stuff professionally, and have noticed that I spend more time on the brake job than most because of the detail I put into it. However, my bosses and I have noticed that I have fewer comebacks with complaints and more satisfied customers as well. I make a bit less on the job, but I tend to get more repeat customers requesting me to work on their cars.
One option you might want to look into is getting a pair of loaded calipers for your truck. That saves you a lot of work cleaning, inspecting, repairing, and lubing. Plus most come with a lifetime warranty on the caliper so if anything happens, can simply swap out.
Long and involved, hope this helps. Hit me up if you need any help. Couple of tips for the wheel bearings, use an impact driver on the small lock screws for the axle nut. They are very soft and the phillip head strips easily. The impact driver will pop them loose without damage. Axle nut socket for an Isuzu Trooper or Rodeo will fit the nut. Might need to file the edges of the pins a little, but should fit. Another option I have seen is a piece of flat bar with 2, 1/4" bolts that are long enough to reach into the holes of the nut run through the bar spaced the same distance as the holes in the nut.