Wont go into gear
#16
Put the nut back on the ball joint stud, loosely. Ideally turn it over so the flat side is on the bottom and the crown is on top. Put the bolt back in that holds the fork to the lower control arm (no need to have a nut on it.) Use a jack to push up on the stud nut. If it still doesn't pop out, hit the side of the control arm with a hammer, don't hit it real hard.
#18
On both Civics I've had, I could never get that pin out. I ended up grinding off the head of the rivet on the U-joint to the shift rod; replace it with a bolt to reassemble.
Edit: As you're just working on the clutch, you may be able to set the transmission on the floor with the linkage still attached. I've never tired that.
Edit: As you're just working on the clutch, you may be able to set the transmission on the floor with the linkage still attached. I've never tired that.