I have a couple inches of water under the hood, back near the windshield where the battery is. Is something supposed to be there to keep it out?

 

Remove the battery from it's mounting bracket,you will see 2 holes with rubber boots,they probably are filled with leaves,weed,cocaine and other debris ,clear it and you should be fine.

when it get clocked up,the water builds up,you better hurry or you're battery compartment will rust and rot away after awhile.