I have a 1989 wrangler. I have 2 problems.
The first is exhaust fumes in the cab. This only occurs when a window is open. It’s the worst when I let off the gas peddle.
The second problem is occasionally when trying to engage third gear it either grinds a little before going into gear or I have to push it extra hard to get it into that gear. Third gear is the only gear with this problem.
For the exhaust fumes I would suggest experimenting with different combinations of open windows to find out what ones work. I would also suggest making sure the exhaust system is as originally designed and has not been modified or damaged. If someone switched sides or added a side exhaust rather than the rear exhaust, that could be the problem.
A correctly installed and properly functioning exhaust system should not allow exhaust fumes into the vehicle. Check for leaks.
The transmission problem sounds like a worn third gear synchronizer to me. Is it easier to get in gear if you double-clutch?
Clearly it makes most sense to find out the source of the fumes. This ought not to be too hard, especially if you raise the car and check from underneath. You can feel with your hand the warm breeze from the leaky part. Knowing the fault will enable you to decide on a cure.
As for the transmission problem, I suggest you start a separate thread so maybe Transman will find your post.