I don't think it switches into limp mode because of low fuel. I never heard of that. But I had never experienced limp mode in any car.
Here some info:
http://grego.ca/limp.htm
I am still thinking that the computer does not get all the signals it needs, or that the signals are logically impossible because there are shorts. cleaning connectors and replacing sensors should eventually fix it. If you can get sensors from a junk yard car (one that did not get flooded) you should meke good progress on the path of eliminating potential causes.
Your situation seems to go along with this:
COMPUTER CONTROLLED THROTTLE BODY LIMP HOME MODE
Many newer vehicles have a "drive by wire" throttle. This means there is no cable or linkage directly linking the accelerator pedal to the throttle.
The manufacturer goes to great lengths to program electronic throttle control to be just like the old style throttle as far as the driver is concerned.
The limp home mode on electronic throttle control WITHOUT a mechanical backup system like the SAAB above, is to hold the engine at a high idle. This idle will be high enough to "limp home" at 30-40 MPH, but obviously can't be driven much before repair.
That's why I suggest you look into the DBW system at the pedal.
And I think your fuel level signal is a completely separate issue.
I suppose you changed the fluids after the flooding? I think I would do that even though the chance for water to get into the crank case, cooling system or the transmission is low.