After swapping a b16 into my Civic the shifter will go easily into 1,3,5, but has issues going into 2,4,R. With the shift linkage off I can shift through all the gears using a screwdriver through the transmission pin/linkage. I've tried replacing the bushings on the shifter with no improvement. I plan on pulling the entire shift linkage and shifter assembly and replacing any worn out parts.

Is there anything besides the shift linkage that could cause this issue, or do you think the shift linkage will solve my issues

 

Sounds like the shifter/linkage is hitting something or you're using the wrong linkage.