What could be the problem with a 1994 Ford Crown Victoria that keeps missing after a tune up with only 65000 miles?

Several things will cause a misfire. One of the most common I see is when folks go to their friendly neighborhood parts store and buy low-cost plugs and plug wires, and then they wonder why their engine still skips. There is a reason that some aftermarket plugs and plug wires are way cheaper. It's ususally that they are junk. Some of these aftermarket plugs and wires especially simply do not work with Ford's high energy ignition system, no matter what they tell you. But lets not jump on that possibilty just yet, but let's also keep it in mind as a possibility. You cant rule anything out. Another thing to keep in mind is that 65,000 miles doesn't seem like a lot, but it is enough miles for anything to go wrong. I have seen engines come completely apart(implode) at less than 10,000 miles. So mileage is not really a factor. A misfire can be caused by a vacuum leak in the intake area close to the cylinder, a loss of compression on that cylinder(possibly a sticking valve), an ignition break down (which includes the coil tower for that cylinder), and a fuel injector problem. If you can get the cylinder to misfire by having someone hold the brakes, drop it in gear and load up the engine, try to isolate which cylinder it is, by canceling out the cyinders one at a time. The cylinder that makes the LEAST difference in the way it runs, while the engine is skipping, is the culprit. After locating the skipping cylinder, you can eliminate possibilities, by switching plugs and wires with a known good cylinder, and see if the problem moves to the other cylinder. You can switch the coils from one side of the egine to the other, and see if the problem moves as well. If that doesn't work, you can disconnect a small vacuum line and again make the engine skip. While it is skipping, spray carburetor cleaner into the vacuum hose. If the skip evens out, you have a fuel system problem like an injector or a vacuum leak. You can eliminate the vacuum leak possibility, by spraying carb cleaner all around the intake close to the skipping cylinder and see if the skip levels out. BE CAREFUL NOT TO SET THE ENGINE ON FIRE! Have something to put out a fire close by. Good luck.