Hey, you handled a very tough fix. Drilling the gearbox and putting in a set screw on that collar is not for the weak hearted!
Using the clamps is to alter the shape of the bracket while the adjustment brace is loose. You can also rehape the sides of the bracket if they are starting to splay.
If the bracket does not move smoothly up and down something is wrong.
I recommend you pull the MPF out;
Inspect the components, make sure all the brackets are there. Some people hack the rollers with washers (not optimal). And, or the rollers are not mounted properly.
Get some photos of all four of the side rollers and the roller contact from the cam. We're looking for any "chew" marks in the brackets / rollers. Weird warps in the brackets too.
If it passes the visual inspection, I'd like to see you gently clamp the base of the bracket in a bench vice;
hook a power source to the motor (12V -20V DC wall wart works well.)... I like 12V because it does not move as fast.
get some movies of the action up/down.... without the optos working, it will just pump up / down... it's really good to diagnose bracket issues like this