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?

As you say . Nothing really obvious there . Bush looks fine . Clearance is a bit tight and a bit more would be preferable but I don't think that would be the noise .  Gears are new and outer good looks correct , dot was downwards . Bush is fitted correct with respect to the lube notch Only other thing , I have heard about it but never had it happen myself is the converter making a noise 

Finally got around to removing front pump. No obvious signs excessive wear or damage.                     Although the bushing seems to be worn on one side but not sure if it's excessive.