Also had some black soot come out of the exhaust. It's like stuck on the floor

 

The black soot is just carbon you washed out of the exhaust. Hopefully you didn't wash out a cylinder in the process. If you were in water deep enough to draw it into the intake, you likely have a large quantity in a knock sensor well since you didn't seal them. You also need to check all your ignition connections and make sure they aren't full of water.

As for RTV, you need the Permatex hardening type around the inner edge of the plug and the point where the wire goes through. The soft stuff or dielectric grease will wash off or evaporate in time, leaving gaps for water intrusion.

 

Ok thanks for clearing that up......I understand how to seal them now...

 

So you think the sensors would detiorate in a year? They didn't go out for 14years previously

 

You didn't use OE sensors or harness. A shorter lifespan is absolutely guaranteed, especially because the Dorman harness uses a harder material in the well cap which does not seal as well. Without proper sealant, you will get water in there.

To get water in the engine via the intake requires you to have water at least on top of the engine valley.

 

It wasnt that high, the water got in the intake because of splashing. There is no way it got in the valley

 

Well, it's your call, but if the splash (wave) was high enough to reach the intake then it almost certainly carried through the engine compartment. Unless of course you have a CAI that draws from behind the fog light or low area.

 

Well I messed with the knock sensor harness and connection a little bit, and it has went away for now. I do have a weird humming sound when I'm doing 25+ I think it may be a hub? And also have some kind of rattling noise when idling or at have low speeds. Any ideas? Thanks