Last week I bought a 2004 Ford Focus. It has 170,000 mi on it. I was told the transmission and clutch were new. Last night, (and this evening), I was trying to teach my daughter how to drive "stick". She repeatedly stalled, bogged and bucked the car. Now the gear shifter seems broken. It will only move straight up and down- loosely. It will not engage. Luckily, the transmission is stuck in 1st gear so I was able to drive it home. Could we have literally broken something?? Last night it stalled and bucked quite a few times with a loud "clunk". It sounded really bad.
This doesn't sound like a problem with the transmission itself, or the clutch, more likely it's the linkage that has a problem. The Focus uses cables to transfer stick movement to the transmission, the problem could be in the stick, the cables, or the cable transmission mounts have come loose. As you say the transmission was worked on recently then my money would be on the mounts, either they were not put back on properly or the bushings failed.
What to do depends on how confident a mechanic you are. If you know your way around you could have a look under the hood, the mount is apparently near the fusebox, you'll need to remove the battery. If that's not the problem then you could have a look at the shifter assembly and see if a pin or something else has failed. If the mount has come loose you can put it back on, there's a couple of videos on youtube about how to do that. If the bushing or retainer has broken then they can be cheaply replaced. If the cables have failed or there's a problem with the linkage then you'd need to think about whether you've got the tools, time, and skill to replace it.
Otherwise, I would recommend taking the car back to the shop that replaced the transmission so they can look at it. If it was recently done then the work should be under warranty, and that would include making sure that the mounts are on correctly. If it turns out a different part of the linkage is busted then they're the best people to fix it.