The wave is completely uniform. It's just like a teeter totter. I could set it up differently to get a "double wave", where both ends go up and down at the same time though too.
As far as the intakes yes, I had to do that to get them to fit. The box was made to just barely fit nano streams. I'm actually very surprised that i was able to get these big boys to fit. I had to dremel the sides off the pumps as well - to the point where where orange o-ring that goes around the pump is exposed. No plastic actually makes contact with the box. This is very convenient as it reduces noise as well.
As far as the box - it is a two chamber overflow box. One chamber functions as a normal overflow - with teeth routered in the top. The other side is for the pumps. Both sides are open top of course.
