Adam you may be learning maintenance cycles here. It is getting close to a year now. That overnight may help with the gen as you questioned. If not you need to check your batts. Is the house 12 volt?
You went from being pretty good to terrible in a matter of 60 to 90 days (some pretty good record keeping too) That is a sign of a possibly bad apple in the bunch.
I would want to know if there is a week battery in the bank dragging the others down. If there is, the earlier you yank it the less harm it does the rest.
I think full timing as you do, frequently on Batts, isolating and then load testing each one separately at once a year should be on the list.