Haven't played this game in awhile, but back in the day my afk/semi-afk setup was something like:
10 large farms with sunflowers - pop in every 4 hrs or so to harvest/breed and replant
Sunflower crate workers non-stop in grana
Afk fish in kama tooth fairy cabin, turn in at valencia w/ trade buff
Imperial cooking - mainly tea with fine scent from the sunflowers and milk tea/eggs sometimes
With manos out now, it doesn't take forever and a day to process mats. Before manos, it was best to choose imperial boxes that didn't have that many processing steps cuz it would take too long to process all that crap. But now I'd probably look into the higher level imperial cooking/alchemy boxes again.
Sunflower crates were decent money and easy cuz they didn't require any processing time like calpheon crates or the expensive metal crates. If I were still playing I might take a 2nd look at higher level crates as well (cuz of manos), or just drop them altogether and gear everything towards breeding crops for stonetail fodder and imperial cooking/alchemy mats. Other things I might look into producing afk/semi-afk would be draughts, and stuff for the new boats/boat gear (whatever is selling well on the auction house).
I have not played for some time, but these are the afk-ish things I would look into if I did start playing again.