Carmy 2004 manual gear running time 5th gear not applying back neutral position what was problem. Please advise

Sit in the vehicle .Get someone to move it back and forth while in 5th gear ,try to disengage the gear either through the clutch or by pushing the gear lever to neutral .

indicates a misalignment of the out put shafts either from loose extension housing bolts , bolts not tension in the correct sequence, worn bearings or selector adjustment incorrect and not fully engaging 5th gear in selection

have the fault codes read and use a quality injector cleaner in the fuel
it could be low fuel pressure , injector problems or accelerator position sensor related

Great to hear. Good Job!

You know the thing is 20, 10 years beyond its service life. Something has lasted twice its projected life and you are disgusted? Find a used transmission with much lower mileage and install it, obviously you have the skills to R&R, or find a rebuild kit and rebuild the transmission. It may be cheaper in the long run to scrap it and find another vehicle.

chances are it sounds like the gearbox section is not in good shape. sorry to say.

Hi:
The shift pattern is pretty much the same on all 5 speed cars. The top row is the odd numbers, 1-3-5
the bottom row is 2-4-Reverse. The center position is neutral

Here is the key: The shifter is slightly spring-loaded to the center position. If you hold in the clutch pedal and pull the shifter to neutral, and let go of it, it will automatically be lined up in the position, that if you pushed it forward , it would go to 3rd gear, and if you pulled it back, it would go into 4th gear.
This way, to start driving, you start out in neutral, grab the shifter lightly, and push it first to the left, then forward. This is first gear, where you start out. when you want to shift to second, push in the clutch, and keeping left pressure on the shifter, pull all the way back . Here is the easy part, 2nd to 3rd. When you are ready, push in the clutch, and just push the gear shift forward , till it hits neutral, and is spring loaded to the middle. Then you just push it straight forward to 3rd, then next shift, straight back to 4th.
Last gear, 5th: push forward to the neutral row, then Push to the right till it lines up ,and forward to the 5th gear. Reverse should only be shifted into from a dead stop. Find neutral, push the shifter all the way right, then pull back towards you. Hope this helps.
Practice a bunch in the driveway!

I assume it's a manual transmission.
If the car will not roll backward or forward in neutral (with or without the clutch engaged) the transmission is most likely locked in two gears at the same time.
This may happen if gear selectors are excessively worn. If you are able to examine the gear selection levers external to the gearbox, ensure they are in the 'neutral' (no gear selected) position when the gear lever is in Neutral. If not in correct position, you may be able to manually reset the levers to correct neutral position and thereby unlock the gearbox.
In any case, if it's happened once, it will happen again, so get the gearbox and gear selection mechanism checked for wear or breakage.

i had same problem it is your cam positioning sensor

time to consider a visit to the junk yard and fit a manual