I have an '05 EX D17 5-speed manual. Recently in the past few months my clutch has been acting up so I ripped it apart a few weeks ago and the throw-out bearing was bad. About $400 and 2 days later my clutch plus a new flywheel was all new and fixed up. But now, in the past week or so, I've noticed my car popping out of 5th gear going down the highways, but it's ONLY when I leave off the throttle at a low RPM. I've tried different things to see when it does it, and know for sure that's the only time it does. It doesn't pop out in any gear other than 5th. I don't any short shifter/mods in my drivetrain at all. Everything is still stock. Now my question is...is this possibly from the new clutch/flywheel or a transmission problem alone?

 

Popping out of gear is often because the motor mounts are bad. The engine shifts around and pulls on the linkage. Also check the bushings at the bottom of the shift lever leading to the rod, if they are worn it might not be going fully into gear