Align the shifter & rods for sure.
If they are out of adjustment, the gears can grind & this has happened to me with 4-speeds & my current 3-speed also.
In my case each time, I set the alignment as normal, then did test drives.
Better, but still not right. I went out one turn with the swivel, reinstalled it & it has been fine ever since.
I had a 4-speed with a lot more miles on it, that one took two full turns.
Your results may vary of course.