Get ahold of Roger on the RC Tunze forum. Although you are using the pump in a 'aftermarket' setup, he may still be able to help you out on replacement parts (if any are required). The fact you are using it in a DIY wavebox will kill any chance of warrenty or free replacements parts though.....

On a side note, how fast are you running the pulse? Have you considered slowing it down and seeing if the same problem repeats itself?