99 Ford contour sputtering and surging at freeway speeds.
 

Have you checked the fuel pump? If you don't have a pressure gauge you can pull the hose near the fuel rail and hit the key without starting, it should at least give you a steady/strong stream

Or filter? Not sure right now if the filter is part of the pump, but some of the older ford models had a separate filter in the engine compartment.

Oddly enough, I picked up my mom's 95 Contour GL (with 2.0L) Sunday to be my daily driver. After driving it 40 miles from her house to mine without issue, I went online to find some more info on the car. Found your post and responded.

The car hasn't been registered for over 9 years so I figured I'd clean it up and take it for emissions (smog) testing this weekend. My son decided he wanted to take it for a spin today, but couldn't get it started. I go out tonight after work and got it started, but it sputtered like it's missing a cylinder. BAH! The battery is near dead so I pulled it and put the charger on it.

Since I hadn't had much time to look around while it was running, it's hard to say what happened in two days of sitting in my driveway but I did pull the air box and everything going to the throttle body. Noticed that the PCV hose going into the air filter box was disconnected and hanging.

Will update after the battery's charge is full.

Update: I'm not sure what was disconnected, but it may not be the PCV -I read somewhere that the PCV was in near the bottom and is only accessible from underneath the vehicle. At any rate, there's a keyed plastic pipe that mounts to the bottom rear of the air filter box runs by rubber hose to the valve cover. Mine wasn't locked into place (or was inserted wrong) and fell off. Freeway driving isn't exactly smooth, I have to look around and see if a rubber gasket is missing. MAF sensor wire was coated in oil or carbon, disassembled and cleaned with carb spray. Still something wrong though, thought I had it fixed and drove the 20 miles to work. Couldn't get it to start after work, not even push starting by pushing and popping the clutch. Something about the long freeway drive makes it not want to start after the engine has cooled. Eventually does start but the idle is horrible, like an old carb engine in the winter until the sucker warms.

Anyway, have you had a chance to change the filter?

should not be using carb cleaner on maf