Let me start off with the bad issues. The first thing I have to say is that the interior door handle design is the worst ever. I've seen many Explorers witht broken handles. Next, I hear a slight lifter knock from the engine. At first I thought I'd just drive it until the engine gives out then do a total valve job, well yeah that was 100k miles ago and hasn't caused any major issues, just annoying once in awhile. Well other than that the car has been fantastic. I just recently changed the radiator and fuel pump just for peace of mind since the car now has 333,000 miles on it and I figured it was time. I really think it could of gone longer but I sometimes use the car the take my 1 yr.
Transmission has been great since day one. I've never done any major work on it.