I'm not sure what the time is for resetting shop items but an hour would be a safe bet.
If I'm looking for a certain rare item, or rather several of them, I will save before checking the shop and reset until they have the item I want. Then if they do not have as many of the item as I need I will go away for an hour and when I return I will save again and check the shop to see if they have more of what I want, resetting until the item appears again.
Early in the game I usually just run around fighting enemies for the hour so that I can level up my skills and so I can try for rare drops from enemies like the Gale rune. Late game when I have access to the entire map I will travel from one area boss to the next looting their chests for extra funds and checking the item shops after each complete circuit. On my old save I have everyone but the knights equipped with the best armor I can buy with their weapons all level 16. The Windspun Armor is the only thing I still need and I have only ever found one at a time in Le Buque. Given how much they cost each it has been a slow process getting them however I have managed to level up all the playable Stars and max their skills in that time. ^_^
If you don't feel like grinding away for an hour you can always just leave the game on and go do something else. Every once in a while I'll watch a movie and then come back to the game instead of playing the entire time.