OK Here goes:
Disclaimer: Don't do this unless you have a some basic electronics skills and are willing to lose the whole thing and possibly burn your house down if you screw up.
The timing of each of the "low" "medium" and "high" settings within the control box is determined by the action of an HEF4528 IC. There are two of these ICs in the box. One controls just the "low" setting, while the other controls the medium and high. The length of the timing interval is determined by a resistor and a capacitor for each of the timing cycles. At first I thought I should try to change the resistor, but because that would have meant changing each of the potentiometers and I am pretty lazy, so I noticed the capacitors were each 22 uF, easy to get at and cheap to replace so I went that route.
Reading the data sheet for the HEF4528 it looks like the relationship between the capacitor and the time interval is linear so changing a 22 uf to a 2.2 uf on the low setting changes the time from 2 to 10 seconds to .2 to 1 second etc. etc. This works the same on all three with the result that a 220 uf capacitor on the high setting lets it run for up to about 2.5 minutes. But It's best to get a bunch of capacitors and try it out yourself. It's even possible that you could make a wavebox work with the stock controller if you can get the timings right.
A lot of the posts discussing wavebox controllers for this pump talk about using a 555 IC. The funny thing is that the controller uses this same IC for PWM for speed control. My thinking is that it's often easier to mod something someone else already engineered than re-inventing the wheel.