Hey! Thanks for getting in touch, and I'm super happy to hear you're loving it. Before I get to answering your question, here's a quote from the rules section onf power tokens:
Removing tokens
If you remove a resource from the map you will also need to remove two power tokens from the city back into the pool.
These tokens should come from the resource but if some have already been moved away, remove the appropriate number from a faction of your choice.
Note that the city always retains at least one power token, even if its last resource is removed.
The emphasis here is on the last sentence. At least one power token remains in play at all times. Granted, it is a note we could add to the REMOVE RESOURCES section as well, just to be sure.
Now to answer your questions:
how do i give power to a faction since there are no resources to be controlled?should i just use use one from the pool and count it as "non material power" like customs or faith?
As stated above: There's always at least one power token remaining.
what should i do when i need to remove power from a faction but theres no faction remaining in the city?
Whenever you're asked to perform an action that is not possible, you do nothing. Granted, the game doesn't explicitly state that and I think it probably should somewhere. I'll make a note.
should i add resources or factions as i see fit sometimes, outright ignoring some of the events effects if theres no way to implement them given the circunstances?
Ex Novo is a very flexible game, especially if you're just playing by yourself. If you feel like adding something because it makes sense for your story, feel free to.
what should i do if i need to remove a resource and the city has none?
This goes back to the statement above: If you're asked to perform an action that is impossible, you do nothing. Though thinking about it, it feels like if you are "asked to do something that is impossible you are free to perform any other action instead" feels more fun, as a solution.
I hope this helps, and thank you so much for reaching out. Oh, by the way - if you have time I'd really appreciate a rating of the game.