I don’t know the 6spd transmissions well but that sounds like an adjustment issue. That’s what I’d say if it was an 02A/J

 

Check shifter linkage, make sure nothing is binding. Also check shifter adjustment, you'll have to remove the air box to see the shifter.

Use dieselgeek videos for reference:
part 1: https://www.youtube.com/watch?v=B5EMACf8tKQ

 

Also, check the alignment in the interior shifter box as well.
There is an alignment hole on the shifter box assembly under the shift boot.
All you need to align it is a nail or small straight pin to align things.

 

Ive checked for binding yesterday there was none, after alot of research last night here are the 2 things I'm going to do to see if it fixes it. 1. Gear shifter alignment. 2. Lube up everything with white grease.

 

Do you know history of this car? It would help with determining what is wrong.

Shifter does not get un-adjusted on its own. Something must have happened (transmission was removed, or hit in the front of the vehicle)

 

I stated I don't know the history, im a dealer. Bought it from a auction. No signs of wrecks. Pretty sure it just needs grease. Probably not an alignment, haven't had time to grease it yet about to do it tomorrow. It shifts fine sometimes. Usually when it's bone cold. When it heats up it starts to act up until its bone cold again.

 

If it all checks out, look at the engine bushings. I have a lot of slop in my rear bushing and am going to get it replaced. Because there are times after I park the car, it doesn't want to go into first and needs the 2nd to 1st shift to get into 1st. It happens are random plus the shifting of the engine mounts makes me think it could be that in my case.

 

Update - greased everything, all gears are back smooth as heck, haven't drove it yet due to having to change the oil. That's my next step. I only greased it didnt a line or anything.