First of all, Welcome!! I love the fact that you started posting with what you posted!!! FANTASTIC!! My suggestions to you are..
1. Check depth before crossing, if you can..
2. When you're sunk, shut the bike down and don't try to run it until you've tipped the bike upside down and pulled the spark plug to get all the water out.
3. I'm at a loss as to why it's running the way it is, but hey, what better way to get a badly running bike than a huge sink hole and photos of it!!!
I'm sure you'll get the runnability issue sorted out.. Take you time and eliminate all the simple things first.. You've got mechanical ability, judging by your last photo.. On the other hand, you've got questionable common sense, judging by the first photo!!
Again, welcome and thanks for the photos!! I wish I had a camera the time I had my CR250 buried in muck so deep I didn't know if I was gojng to be able to get my boots out of it.. We've all been there and while the bike might not run quite right today, you'll get it figured out and be laughing at this for years to come!!