Our 1999 Mercury Villager has scary noises under the car, sounds like the frame is breaking away from the body. Also, the road noise has always been loud and very noisy when going over bumps in the road. I knew better, as I would never under any circumstances purchase a Ford product, thought this was really a Japanese auto. I sat through a court case against Ford a few years ago and was very surprised at the things they have done to save money and lower quality and safety.
I own a 1997 Villager van, and have had similar issues. The clunking noise on the front end (referred to originally) may be the upper ball joints on the front end. Ours needed replacing a couple years ago. The power door locks are unpredictable - ours seems to lock itself mostly. I've read elsewhere that this may be corroded wiring connections inside the door panels causing intermittant issues. Our check engine light is on constantly also - I check it, and it's still there. Actually they told us we'd need an upgraded PCM since we moved this van from MI to CO, and it can't handle the altitude. Needless to say, it's hard to justify a $700 electronic box to put out a yellow light. Every now and then it does go out on it's own. (that's when I worry). But I'd have to say - beyond those typical issues, it's a workhorse of a van. I use it more like a truck actually. Good for hauling wood, etc. Good luck!
I am also having a problem with a loss of steering with my 1999 Mercury Villager. This is really disturbing me because it happens rarely, but when it does, the steering wheel is so hard to turn. I should also park the van, but I cannot at this point, because we need the van.
The van also has a big problem with rust at the bottom of all the doors, which drives me crazy, because the van is a gorgeous vehicle and is high quality throughout, other than the problems I listed above.
The drive train is top notch when it comes to dependability, power and smooth quiet acceleration.
I love the van, minus the rust, and the steering problem.