My guess is that one of two things happened:
- The vinegar refreshed the rubber seals and they have stuck
- The bottom of the plunger didn't get hooked on the nub of the linkage that comes through the pipe
If you can get back to where the linkage comes in to the pipe, there should be a threaded collar that holds it in place. Pull that bad boy loose and the rod should pull out of the pipe. If you have enough room there, you can stick a small screwdriver in and try to push the plunger back up. You'll notice that there's probably a loop on the bottom of the plunger assembly. As mentioned in point #2 above, the nub of the linkage should extend through the drain pipe and into that loop. This will allow the linkage to move the plunger up and pull it back down.
If that all fails, you probably need to replace the drain pipe assembly. They're relatively common things to buy at hardware stores, but the replacement process can be challenging. If this makes you nervous beyond your capabilities, I suggest calling a plumber.