How did that happen - a flooded road?   Yeah, water doesn't compress, although I wouldn't have thought bent conrods, would make the engine run poorly?   An inspection camera down each bore, could be helpful maybe? A leakdown test, would show any bent valves. Plus as @deankxf says, measuring each cylinder stroke with a plastic stick or similar, would be useful!   Did you replace the oil too - I imagine that would be full of water also?  

That probably would be the go, although if most of the guts are ok I was maybe thinking of doing a turbo build (nothing too crazy just put some stock xr6t parts on it if i can find them cheap)

depends i guess.  if it was mine i'd probably chuck another engine in.  @Thom may know if a bore could crack from it, i'd expect it possible, so therefore having the engine block crack tested might be something to do. 
i wouldn't expect anything else, but i also don't know heaps about this issue. 

Ill give that a try. If con rods are fked what else needs doing or could I get some rods and go?

bent con rods are likely.  there might be a way to check by dipping something down the spark plug holes and rotating the engine by hand.
if one or 2 are lower on each top of the stroke position  then bent conrod is confirmed. 

 

3 days ago I learned the meaning of if its flooded forget it and my fg falcon got the engine flooded with water. I pulled the plugs out and got the water out of the cylenders but it wont run now and the engine sounds very lumpy. Im planning on running a compression test but what kinda damage am I gonna be in for. Im already suspecting bent con rods or bent valves but I dont know how to check that apart from just pulling the head and looking at it. Any help would be much appreciated!

Fired her up today, no noise so definitely coming from the tranny. Waiting for some parts now to put it all back together.

Yeah I'll do that just to be sure.     Yeah it did, I bought the transmission as "suit rebuild" and the convertor came with it. I fitted to the car and got 5000k's out of it before I had that and the engine rebuilt. Was pissed off when the noise was still there so chances are there's something still faulty or I should have taken more care when putting it all together.  

One way to find out, going to get another torque convertor which I should've done in the first place.

Try something. Bolt the spacer plate, drive plate, and bellhousing back on and run the engine without the trans. Curious to know if there is any noise WITHOUT the auto.   Also, did it make the same noise prior to the auto rebuild?