I stuffed a tapered punch in the pickup tube so the threads wouldn't distort and then pinched the tube in a press with a socket on the spot of the tube where the bolt was hitting. Sideways like you know, so it put a curved indent on the tube.
This was on a 1/2" pickup tube with a 4.375" stroke 2.2 rod journal setup. Was a lot faster than waiting for the boss to cut and weld the tube to make it clear