There is no official ruling, so you will have to house rule it
There seems to be some concern with Fantasy Flight Games slow FAQ releases and lack of designer feedback on rules clarifications. One do the designers, Richard Launius, has answered some questions sent directly to him, but they aren't considered official rules clarifications.
This particular question has been asked on the FFG forums (Q3), but without an official answer. The question is also on BGG, but again lacks an official response.
Neither the revised rules nor the FAQ address the timing of the application of the Ancient One's (AO) abilities and Item effects. So, you have two choices:
- Apply the AO effect first: This would mean that a Healing Stone would restore your stamina to the maximum (5 in your example). It also means that if you are 1 stamina you would be devoured. Which means that while nothing in the rules prevent you from using the Healing Stone at 1 Stamina, you probably wouldn't for strategic reasons.
Being Devoured - If at any time an investigator loses sanity or stamina that causes him to drop to zero or less, he is devoured.
When an investigator is devoured, that player adds one doom token to the doom track and returns his investigator card and marker to the game box. [...]
- Apply the AO effect after the Item - This would mean that Healing Stone would restore your Stamina to the maximum minus one (4 in your example). It also means you have nothing to fear when using Healing Stone at 1 Stamina.