Deleting the EGR is common when removing all the smog crap (pump, check valves & hoses, solenoids, vacuum lines, pipe in back of the heads, etc.) Deleting the small water lines is just to clean up the engine bay and remove the chance of a water leak if the TB gasket ever fails. Some say the water supply to the spacer is to help cool it down in the summer and some say it's to keep the TB from icing up in the winter... I think it's for both. But I don't have them hooked up in my car because it's never driven in the winter and the cooling effect can't be too great because the temp of the coolant is about 190*.
And here is a good close up pic like I promised.