Rebuilt tranny shifter alignment problem.

[SiN360]

Ok I have an 87 prelude si, it has an A2K5 tranny. My father in law helped me rebuild it since he has done transmission's before just not a honda. So we got everything done but now we can't seem to get the shift rod lined up correctly. It's sitting to much to the right and it super hard to get into 5th and reverse. I finally tested the car today and it goes into 1,2,3,5 and reverse but not 4th like it not sitting correctly not catching 4th. It's sitting real close to 1st and 2nd when in neutral. Sorry I wasn't getting not help at preludepower so I'm hoping someone can help me here. I had tried to re adjusted then I was sitting to much to the right towards 5th and reverse. I have centered the shifter with now luck.
Does rod in the tranny have to be in or out when installing everything.

Thanks in advance