Rubber piece on caliper pin
I just went thru this with my 03 Explorer. Checked the factory service manual and Motologic (a mechanics resource).
The factory diagram shows the pin with the rubber sleeve to be on top. But that is looking at it from the back side of the driver's brake rotor. It's the same caliper bracket on the left and on the right, so if you set the pins in the way the factory shows you to (regular pin on the bottom, and pin with the rubber sleeve on the top), that is correct for the driver's side. For the passenger side, it IS the opposite.
Easiest way to do this is to assemble the caliper bracket and pins like the picture shows for both sides, and then just bolt the brackets on. You'll find that in order to bolt the bracket onto the right side, you have to flip it over. So yes, the rubber sleeved pin is on top on the driver's side, and on bottom on the passenger side.
I had regreased these a year ago, and when I took them apart today, I found that the one with the rubber grommet had seized. It wasn't water or rust or anything... the grease still looked good even. It was that the rubber sleeve had moved. So I'll be double-checking from now on, a few months after install. This had caused one pin to not move, and wore the brake pads unevenly on the caliper piston side.
This time, I used less grease. Just a thin coat. I made sure the pins were clean, and not greased underneath the rubber sleeve. I gave it a light coat of grease over the pin and rubber sleeve, and gently rotated the rubber sleeve/pin into position. This kept the sleeve from moving on the pin. We will see if this works. The scary part is that I'm pretty sure I did all this the last time too, and somehow my process led to uneven brake pad wear and a seized pin.
It is true that the two sleeves are different sizes. You can feel that they fit better when you assemble them as described here.