not to be redundant but have you taken the belt off the waterpump and ran it for a few seconds (i repeat, only a few seconds as its only safe for about 15 seconds) to see if the engine was knocking and not the waterpump? if the oil pan was damaged i would have removed the pan and inspected everything, i mean you only would have had to have replaced a cheap gasket if everything was fine. then again if something wasnt you just found a problem that would keep you from asking questions as you are now, but its okay, you live you learn. a loose oil pickup tube making a knocking noise, i doubt it very seriously, i hate to say it but i think you may have bought a bad motor. the only way a loose pickup tube would make a knocking noise is if its rattling around and smacking the rods as they go down, and another thing you may look into just incase, take the oilpan off and make sure the rods arent smacking the dent in the oilpan. my old integra hit a pothole, bent the oilpan and stopped the engine, i pulled it from the hole and seen my oil pan was bent, started it up and the crank pushed the oilpan back into shape but made a lil scraping/slapping noise. i lived w/ it as i was going to pull the engine and make it a ricer/racer anyway at the time, but ended up selling it later as the timing belt jumped and skrewd the valvetrain. just minor food for thought.
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