I had nearly the same issues after a deep water experience. Heavy rains left 10 inches of water in my commute path. Even though I went through it slowly, every error message possible appeared on the dash when I shut the vehicle off. All of the fail-safe messages came through. The dealer determined the engine harness shorted out. Fortunately, my comprehensive insurance covered the $1837 bill as storm damage. The technician did tell me though that all of the harness connectors seemed "dry", missing any silicone grease to aid in sealing them. About a year later, I got the transmission fail-safe warning after going through a car wash with an undercarriage spray. It dried out the next day and went away. A few weeks later another heavy rainstorm triggered a full shutdown of the transmission to the point I couldn't get it out of neutral. After letting it dry out for two days, I was able to get it to move and got it to the dealer. The harness connector to the transmission was absolutely full of dirt and moisture and no seal left. They cleaned out the sockets and polished the pins and I haven't had any problems for more than 100,000 miles.

2002 X5 3.0 305,200 miles
2014 428i 19,500 miles

2004 325i sold at 123,600 miles
2001 325i sold at 66,000 miles

1970 Firebird Under restoration