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Two day update and the car and all electricals are working perfectly! Now back to the start of my problem, the 2" of water in the battery recess. When I changed the battery, I cleaned the area completely after I had vacuumed all the water out. I drove the car in dry weather to work this morning, it rained while I was in the office with the car parked in the lot, and then I drove home this evening in the dry. When I opened the trunk, low and behold, I had a small puddle of water from the rain this afternoon. I know it's not from driving the car and couldn't tell visibly where it would be coming from. Can anyone tell me where to start looking as I am going to leave the spare out so I have easy access to find this. Thanks Guys......
Well, I hosed the car off this morning and low and behold, a trickle of water on the drivers side coming from the rear light area, clear as day(see photos). Time to pull the light and get it fixed. Thanks for all the support.