Sounds like maybe a fluid change would help. Which I don't know why they wouldn't have changed it when they did the clutch? But also maybe check the fluid level, there is a bolt on the front of the trans, you should be able to just stick your pinky finger in and feel it.
Or the syncros are maybe going bad. But also check the shifter cables too.
2000 SE wagon 2.0l Zetec.