29,000 miles: Rear wiper was already malfunctioning when I bought it - wiper blades would not wipe evenly across the glass. Sometimes the wiper motor wouldn't start at all. I understand this is a common malady among 2nd-generation Explorers. I have not gotten this fixed.
40,000 miles: transmission "flare" between 2nd and 3rd gears. Occasionally, O/D malfunction light would flash and the tranny would go into "safe mode" and remain in 2nd gear only, not upshifting or downshifting. Research tells me this is another notorious problem among 2nd-gen Explorers. I have not gotten this repaired.
50,000 miles: Sunroof grinds to halt upon opening. It also doesn't ride smoothly along the rails, jerking here and there while being opened/closed. Occasionally it will not close at all, but will prop open in the Vent position. I have not gotten this fixed.
50,000 miles: The dreaded lower manifold gasket leak. Recall the O-rings that failed on the space shuttle Challenger? Similar thing here. Gasket shrinks when engine is turned off and gets cold, so when engine is started up again, the seals let in too much air, throwing off the oxygen/fuel mixture. The engine computer tries to compensate by making adjustments, but it's no use - the engine shudders and idles rough for about 10 minutes until the seals have warmed up and expanded to seal out the outside air. I got this fixed by dealer under Ford's OOM12 technical service bulletin and covered under a "secret" warranty (not a recall, so Ford wasn't obligated to tell customers about this and they just replaced these gaskets quietly as they were brought in).
Side steps are rusting badly.
Fuses to 12V accessory jack and cigarette lighter keep blowing. I only use them to charge my cell phone.
Interior trim panels rattle and creak, and fasteners coming loose, prolly because of the Explorer's bone-jarring suspension.
Hood paint is peeling; roof paint is cracking and surface rust has appeared in the roof water channels. Ford acknowledges their painting methods were faulty, but offers no recompense. Apparently the hood and roof are made of aluminum and the paint method used doesn't allow for good paint adhesion to it (as opposed to painting on steel, like the fenders and doors).
Hood latch and cable assembly were replaced by dealer because I wasn't able to get the damn hood open.
6-CD changer stopped reading CD's. I replaced it with an identical unit and it worked fine.
4" diameter rusted-through hole in engine bay wall right side.