Need Help Pleeease!!!

My bike is an 07 King Quad 450 Fuel Injection. After about an hour of riding I put it in a mud hole, maybe a foot deep, and worked the bike kinda hard. I started noticing that the idle was getting low and it would shut off sometimes and was hard to start. The fan came on so I took off down the road to cool it down but it wouldnt hardly go. It was backfiring and eventually got worse to where it would shut off completely.

I thought it might be the fuel pump and it seemed to crank up better if I turned the key off then back on and let the fuel pump prime. I also thought that it might be the CDI box going bad.

I let the bike sit for 3 hours and completely cool down and took it down the road and it ran great.

Any ideas or suggestions? Please help.

I forgot to add that it started smelling funny, like a new engine smells when you run it hard. I've smelled this before but only when I run it wide open.