Before you tear off the oil pan, confirm the oil pressure with an accurate pressure gauge. Don't rely on the stock gauge. Compare the oil pressure readings to what's in the FSM. If the readings are within spec then clearance between the oil pan and the pickup isn't the problem.
Did you ever take the timing belt covers off before dropping in the TT engine? Do you know when the last time the timing belt was replaced?
If your having trouble pinpointing the source of the noise, buy a stethoscope and probe around the engine until you find it.