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When you replaced both "drain plug things" do you mean you replaced the firewall drain grommets with "newer" grommets? OR, did you do the drain reroute? A little clarification helps here. If you just replaced the grommets then likely they are failing again. I will not get into the debate over those who continually replace the grommets with Nissan's "newest and best revision" vs. the drain reroute mod. The grommets are a crap design, period. Again, what exactly did you do?

As for other points of water ingress: check the cabin air filter. If it is wet then the cowl seals have failed/ likely deteriorated due to age. Being you recently removed the cowl for the battery change this is likely. Also, there is a large grommet near the battery that the main wiring harnesses pass through.

If the BCM is wet it could be experiencing some weird behaviours- like the excessive power draw. The only way to know for sure is to check the BCM/ wiring connectors for signs of water. Many have had luck by removing the BCM and allowing it to dry out fully. Then, making sure everything is clean and free of any dirt/ corrosion, they reconnect and all is well. This is just luck of the draw, however. In the event the BCM needs replacement then, yes, your key fobs will have to be programmed to the replacement BCM. A qualified locksmith should be able to perform this at a reasonable price. A dealer can but will cost you 3 arms and 8 legs...

Only you can decide if you want to sell the car or not. I have never been a fan of Carvana though others may have other opinions.