I agree with what has been said

that it should be ignition problem rather than water entering into engine. If water has been sucked into engine, your engine will be gone: simply because water is non compressable and huge pressure will crack the block.
With or without bottom shield, there should not be a big difference for the ignition coil performance. Therefore, I think have the ignition system checked is a good idea. Of course you need have the bottom sheild installed if that was missing.