A water pump is normally used on a slow boat, a boat with a clutch. Most "race pipes" don't need cooling. The WHH water cooled tuned pipe uses water to cool the connection between the header and the aluminum pipe, the silicone tubing.
You do not need to use the water pump. You connect the water pick up to the bottom water inlet of the cool cap. Then connect the upper water outlet of the cool cap to the water exit or onto the water outlet of the exhaust header. You don't need the Iso block to have the tap for the water pump.
If you remove the cool cap DO NOT tighten the cap on with the tiny hold down bolts. Use a 10mm bolt of 3/4" to 1" long and a fender washer. Tighten the cap down then screw in the tiny bolts with a little blue lock tight on the threads. If you cannot get a 10mm bolt a smaller dia. bolt you can install the cooling cap using a a longer bolt the fender washer and smaller washer and nut on the inside of the cylinder when it is off the engine.
Why do you need a tuned pipe 17" long? How did you measure the length? Normal way is to measure from the exhaust port (outside of cylinder) around the centerline of the header to the first widest part of the pipe.