I would agree about the battery size. HOnda has the habit of installing really thin small capacity batteries sometimes…My girls 98’ Civic is an example of this. She does NOT drive it far enough to work each day…so that little batt is constantly in a state of low charge. How long do you run the car each day? If you have the room to fit a bigger batt in there I would do that…ALSO check the state of your batt terminals…they need to be clean and greased to ensure proper charging of your battery.
If you do opt for a bigger batt buy a Dry cell battery like an Optima battery…you can mount an optima upside down over your head without worry of leaking. I have done many custom battery relocations in vehicles…usually locating them to the trunk…at that time we can put any size batt in the car… But I know you dont want to do that…if you have the room for a bigger bat under the hood in or near its stock location look into that because it is a very logical idea.
Make sure your batt terminals are not corroded and if your commute time is very short then you will ALWAYS hae this problem with a stock size battery and even the bigger battery will struggle because you dont allow it to charge long enough.