There is a member here "Top Hydraulics" that you should talk to.
From what I am hearing in that video, it is a fluid issue but it COULD be electronic, in that the TCM or limit switches are messed up, causing the pump's switching valves to cut off flow before the cylinders have moved as designed.

I BELIEVE the system is self-priming/adjusting, so low fluid that is refilled should not mean that some process has to be followed to "clear" the lines, but I am not sure.

It just seems to me like the fluid is low/not pumping right.