As far as the header install, you have a misfire somewhere, and its bad enough that the car is yelling at you when the SES blinks. check all your wires to make sure they are going to the correct cylinder. Also, if the wires are old, then replace them.
As far as the standing water, is it just water, or coolant? Do you have the aluminum gasket? When I had my SD, it did let a decent amount of water into the engine bay. I actually have a set of foam inserts i made to block the heat extractors when the car was just sitting. If you're interested, lemme know, I don't need them anymore.
