I save my stamina potions for events. . and then use them on Mondays for the week of the events. .
or you c*e them for the monthly event things. . .
I mean, make the most out of them, right? With the monthly events, you can get more threads. . .
Especially if you are f2p, you have to be patient and make wise decisions.

Which ninja fragments do you collect that is taking so much of your stamina? lol. . .
And it shouldn't be forever. . .I mean, once you hit 4-star or 5-star. . . eh. . .

why refine runes over threads?

If you want to, use all your stamina pots right now. I guess if you want to assume our suggestions and examples as absolute, divine commands to shove our ideals down your throat, you can do that.
Who cares about missing all of those monthly event points AKA threads and runes, right? Who cares about using them for juicy events like Ramen Event or Character Plate events in the future that may hold even better rewards. Lol, after all, these suggestions are just us forcing our ideas down your throat and not us giving you advice on the most efficient and smart ways to use stamina potions.