I also have the open air cone LCE K&N air filter and I took out the battery and that is where the air filter is (shortened plastic tube and rubber hose) cause of a electric fan. The battery found its way to the bed in a boat battery box. The only way you are gonna get water in it is when you cross a creek that is as deep as the air filter, which by the way is the same height as a stock box. If I was going to make a submarine I would get a snorkel.

I say let that thing breath. Leave MAF alone put on mods like I did and do a full tune-up (plugs cap rotor, etc...)like I did when I replaced T-chain, LCE cam and everything else. My truck runs great, don't see why yours shouldn't either, oh and I run 89 octane gas.