As viewed from your first picture: There are 2 different stamped rocker arms, a left and a right. They should an L or an R stamped on them. For EACH cylinder, L is on the left and R is on the right. They are not related to intake/exhaust valves.
The notches on the rocker arm shafts are on the left sides of the heads pointed downward [toward the cam]. The rocker arm shaft washers are correctly placed.
The scraping of the pushrod on the cylinder head is a giant clue. I would pull the heads and check things before I pulled the motor.