I only have one ear so it's hard for me to find direction of noises. I would think when the noise occurs you could pinpoint where the noise coming from. I too would suspect the toilet bowl leaking down to the bowl which you should be able to see water movement in the bowl or put dye in the top tank and see if it migrates to the bowl. This would be timed event from the last time you flushed, so you should be hearing it a about the same time you last flushed to 2:30 am. Meaning you should also hear it during all hours of the day and night related to timing?
The flapper valve or seat could be leaking slowly taking hours to move the float enough to refill the tank. If that is it? It will eventually get bad enough to refill more often. IMO toilets need to be rebuild (rubber seals and flapper seat) replaced every few years depending on how good or hard the water is.
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