I have a whirlpool bathtub and the pump went bad feb 2009- finally got it replaced 3 weeks ago. Flushed out the jets (that was nasty) an now I have brown water coming from the hot water tap. It is the only place in the house brown water comes from and here is some sediment coming out as well. I've filled the tub 3x now with this.. Any idea how long I need to flush this? Or is there or a more pressing concern I need to address?

Sounds like you need to start a maintenance schedule.
For long life and fewer troubles you should keep your heater clear of mineral build-up by FLUSHING NOT DRAINING on a regular schedule. Attach a hose to the boiler drain at the bottom of the tank. With the pressure on, open the boiler drain and let it run until the water runs clear. You will see a spurt of red,(rust) followed by white or yellow grains,(lime or calcium carbonate). This shouldn't take more then a few minutes. Do this monthly to keep it clear. Now flush out your hot water lines on ALL fixtures that are affected . Now pull each aerator and clean the screens. Be sure you put them back together the same way you took them out. Don't forget to flush it out every month. Your heater will thank you for it. Hope this helps and thank you for rating my answer, Tom