Recently head gasket blew and had water in the cylinders, it may have gotten compressed.
Could it be the connecting rods?
To answer the rest.
Unless there was a considerable amount of water in a cylinder, the rod should not have been bent enough to be making a noise. If it had, it wouldn't make noise for long, before the engine ate it's lunch. Is this a thump, or a knock? I consider a thump a low tone noise, in contrast to a knock which is higher in pitch. This only occurs at idle? Another characteristic if it were a rod, would probably be an increase in the noise as the centrifugal mass was emphasized, like an increase in engine speed. Was there intermix of coolant and oil during this head gasket problem, what was the symptom?
yes coolant and water got in the oil and yea its a thump low tone sound at first it was a ting from the valve train then the gasket blew and when that happened it made a very loud ting sound after it blew. Thats been fixed but now it has a low tone thump
we had to get water out of the cylinders. Would I just have to replace the engine?
You are dealing with a high performance engine, with close bearing tolerances. Dependant upon how long there was waer in the oil, may have been catastrophic to the bearing surfaces. Not being able to hear the noise, that is only a suggestion. Get a professional opinion. It sounds like lower end bearing noise, though.