My 2006 diesel Jetta's manual gear shift is not working properly. It's hard to pull out of reverse and it sticks getting into first and second. After first and second shifting is simple. I'm sure it's not the clutch. My dad has temporarily fixed it before. It's starting to act up again. (Something was lose under the hood) what do I need to replace to fix this problem? Before my dad fixed it, it wouldn't go into gear at all.
That sounds like the gear linkage - i.e. the physical connection between the gear stick in the cabin and the gearbox itself.
A quick Google suggests that the Jetta has a cable linkage, which may need adjustment - Bowden cables stretch over time, and so become loose.
This page describes a shortcut to the official factory method:
Have a helper move the shifter inside the car while you watch the shifter assembly on the transmission .... Fore-aft adjustment should be the cable on your right when standing in front of the car, looking down, ... Left-right adjustment should be the cable on the left ...
... On the mk5 Jetta and the mk6 Golf you must remove the engine air filter box for clearance ...
Pull the black ring back to compress the spring .... This will expose the shifter cable end and release its threads from the threads on the cable. Move it forwards or backwards 1 thread/notch to "skip" over the threads and then release the spring to clamp the end onto the cable threads. If you wish to lock the springs in the compressed position, turn the black plastic ring. This is not necessary if you're just moving the end slightly - just pull the ring back, adjust, and release.
They also have a link to a Youtube Video