The main problem I was having was that the balls were bouncing around in the hands too much. Sometimes they would bounce out, but also sometimes they would not settle down in time for the next throw which would then be messed up. In order to get around this problem, I figured I should add some material to the hand to prevent bounce. I spent some time dropping metal balls all over everything in my house to see if they bounce. They mostly bounced off of everything including foam, so I decided to order some butyl rubber tape online, which is supposed to absorb kinetic energy.
Here is the tape:
Here I have applied it to one of the hands:
And then placed a plastic layer over it because it is kind of like putty.
Here is a closeup of the parts:
The butyl tape worked decently. After I added that, I was able to keep the robot juggling 3 balls for over an hour, and I was also able to get a decent run of 4.