If the LCD is visibly flickering then the chances are that you are clearing the LCD screen on each loop. Simply removing the clear statement and just overwriting will get rid of the flicker.
Also, if the sheild is blocking the pins then just make yourself some leads to connect it instead of plugging it straight in on top of the arduino.
What are you hoping to achive with the Aquarium Reef Controller?
Can't really do much more without seeing your code; any chance you could post it?
Chris