Shaking in engine, attempted to solve myself and have ruled out a large number of possibilities

I have a 2003 Ford Taurus SE with the Vulcan 3.0L EFI 6 cylinder engine. I have recently made many repairs on the car as it's somewhat old and sitting at 120k miles.

I ran into some flood water about 4-6 inches and drove slowly through. Minutes later I had a flashing check engine light. I knew this probably meant a misfire. It was, I had a code for a misfire on cylinder 3 and also one for the crankshaft position sensor. I replaced the spark plugs, coil pack, and wires and the engine seemed to shake less, but upon viewing the engine I noticed a LOT of movement when shifting gears. So I replaced the upper engine mount (dogbone).

With this I am currently confused. The misfire seems to be gone, but the shaking is still VERY bad. The engine feels weak and like it's struggling. There is visible vibration in the steering wheel. I don't feel like the crankshaft position sensor could cause all this could it? And that's really all I needed to replace the whole time.

Any help would be greatly appreciated. Thanks in advance!