old dirty transmission oil
Old dirty transmission oil can cause issues when shifting, so if you haven't changed your transmission oil in the last 4 years, it's time to do so.
Click HERE to see the how to video.
If your gear syncro is worn, take it to a mechanic to be inspected and replaced if necessary.
worn pilot bearing
Over a long time the pilot bearing on the clutch can wear and cause grinding.
Inspect it and replace it if necessary (must remove transmission, so best to take it to mechanic)
If your engine and transmission are loosely bolted together, replacing the engine mounts can solve the issue.
There is no way of knowing this unless you change the motor mounts, as you should do after a long period of time because they wear and cause the car to shake.