I removed the ratchet top in order to replace with another. When I placed it onto frame I bolted the trans and installed linkage. I tried to shift the gears and it would lock up as if it was hung between gears. I assumed I had made a mistake and removed the ratchet top. Then realized there is a tool to align the shift dogs. I had had it off years ago and replaced no problems. Every picture I see the dogs are aligned. Mine are not they are pointing in different angles not directly in line. I removed the forks to see if I had broken a tab on fork but everything looks to be in order

 

The shifter forks are aligned to the shift drum. There are shims on the shifter forks that you can +/_ in order to keep the spacing as close to equal as possible on the main/countershaft. The shift drum tool ensures the two get you through all 4 gears. Sounds like the shifter forks need to be re-shined to align with the new topi and shift drum.

Some guys do a visual and wing it. best is still following the manual and use the shift drum tool.

 

picture up what you have the way you explain it may not get the right answer