I can say with 99.9% certainty that the 4.0L coil will not work on the 3.0L. We had a 2000 3.0L Ranger for about a year that my cousin gave us for.parts thinking it had a bad transmission. It wasn't a bad transmission, but a combination of bad coil, bad fuel pump, and needing a tune-up. I'm almost certain that our spare 4.0L coils.wouldnt fit, but we still had Mom's old 3.0L Taurus in the back yard. We fixed cheap, and flipped cheap to someone that needed a truck.
Yes, the roof rack can be mounted on a camper shell. Seen it done several times and I've thought about doing it myself if I can find a decent ARE shell around here. I'll be saving the one off my donor explorer just in case. IMO the Mountaineer rack looks a little better, but the Explorer rack is probably more functional. Either would work for me since it probably wouldn't carry more than a canoe or kayak.
Not discounting the Explorer skid plates, but I'm not sure about fitting them. The Explorer frame (96+ at least) is wider than the Ranger once you get aft of the front suspension. Might work, but might also be too wide.