When you use the y-Filter, the gunk goes into the filter and not the pump. I never get all the gunk that you get. Maybe you have some other problems going on. I never have pH spiked like what you are saying. I also own a few undercurrents and they are complete garbage. They don't even supply enough air with their air pumps. I'd be more worried about the size of their air pump than the water pump.
That is not my pump i am just getting going on a under current set up