Couple things here:
The FJ is not designed to take on water. It might have rubber floors, but there is material that will trap water underneath the ruber, which will result in smelly mold in the interior. There are floor vents for the heat/ac under the seats that will take on water as well. Once you get water trapped in the interior you can forget about getting the smell out.
ECUs can be relocated and waterproofed, this is not something for a rookie to do. You have to take into account many things run off resistance readings, and extended wires to the ECU can affect the numbers it sees, making it very difficult to have things work properly. Your better off doing a stand alone ECU for fuel injection that is designed to be waterproof from the start (like chevy's factory marine engines).
There are tons of wires everywhere in the FJ Floor, doors, dash, etc, and none of them are designed to be water proof. A couple water shorts and your down to salvaging the vehicle for parts because the cost of a shop to fix all the shorts would cost more then the threshold to replace the vehicle for insurance cases. Fuses might blow (saving the wire from total shorts) sure, but the residual wires that got wet will corrode, and short at a later date. The worst job I ever had to do was fix a wiring harness on a almost brand new vehicle that the owner had flooded out. 7K+ dollars and no guarntees it would last, because I had only fixed what I could get to without taking the whole car apart.
All the vehicles that last when submerged are typically much simpler designs. A carbed big block with a water proof distrubutor will run under water as long as the water isn't higher then the snorkel. running marine engines with water proof electronics will work too. You also have to worry about water getting into the transmission/tcases, diffs, etc.
I have been in some deep water and never had water coming into my truck, but then again I have a lift/big tires and I don't go in water thats much over my rock rails. If I wanted something that would foard deep water I would have bought a vehicle with no interior, oil/pressure fed guages instead of electrical, etc. Military humvees leak like a blown damn and don't have any wires running around, they run diesel engines that are more capable of running in water, and have very minimal electronics. Thats what you have to have to play submarine with a car.