I am in the testing phase of the software and got a little ahead of myself when i went to test. Long story short, i had a loose thruster penetrator. The enclosure filled with water quite fast and sunk the rov. I pulled it in and the enclosure was 90%full of water. Removed the batteries and headed home. Fearing i had fried everything i was not in a rush to conclude the bad news that i was about to spend more money. The next day i pressured up and air hose and began blowing hi pressure air into every little section inside. i was sure i would be replacing the pixhawk and the raspberry. 30 mins of air into every spot and i decided i was going to check it out. So i hooked a battery and laptop up and what do you know, everything works PERFECT! What a relief. its not the end of the world if you flood it.
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Hi @SaferHarbors,
Sorry to hear your test ended early with a flooded enclosure - that’s never fun.
I’d recommend having a quick read of this comment for an overview of how to clean off electronics that have gotten wet, to reduce the likelihood of corrosion and electrical shorts 
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Guessing that was fresh water you flooded it with. Salt water is much less forgiving. After any flood you want to get the batteries disconnected as fast as humanly possible, drain the water, spray it down with alcohol and pray.
Correct on the fresh water. I had about 150 feet to pull in. Everything seems to work perfect now.