Pentair mastertemp 300 leaking water

Help! My master temp 300 is leaking water from the blower/air exchanger port. The heater is only 2 years old but unfortunately, while out of town this week my water level fell below my skimmer and I don't have a bottom drain. The pump must have ran dry for at least a couple of days. I have a salt system with a check valve to prevent back flow but I don't have one behind the in-line chlorinator. I think the chlorinated water may have flowed in to the heater and sat causing the heater parts to rust. I took the access panes off and opened the combustion chamber but I'm not certain where the leak is coming from. My guess would be the heat exchanger.

I'm considering changing the exchanger out myself for $600 instead of paying roughly $1000 for someone to do it. Anyone have any thoughts on what may be causing the leak? If it is the exchanger, how difficult is it to replace? I'm mechanically inclined and have no problem working on things. Please, all ideas and suggestions are welcomed.
 
Hi Uribe. Changing out the exchanger is not hard but it is time consuming and require the entire heater to be disassembled. The 3 critical things to look for are. Take care not to break the ceramic igniter I usually remove it first Be sure to replace all the gaskets in the kit. Lastly, putting it together wil require using high temp silicone sealant, which I usually get from an auto parts store
 
The kits that I'm looking to buy come with gaskets and the high temp silicone. Just to clear, the master temp I have is one of the newer ones and has a combustion chamber that looks like a pot. Do you have any other ideas on where the leak may be coming from or do you think it is the exchanger?
 
If you have water coming out of the blower than that usually means the can is full to the brim of water. Remove the bottom bolt on the manifold and see if water actually comes out. I suspect it will which means your heat exchanger has been breached and it's done for. Too bad if you think it's chemical damage as if it still had any warranty left, you could get it covered.
 
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