I'm sorry you have had no response.
I think you are on the right track about removing from the container and repotting.
I'm sure you also inspected the root system at that time and didn't see any issues.
I don't know if gnats can cause these problems but they need to be eliminated. Because this is a fruit tree and you want to eat the fruit, I will suggest using this. https://www.summitchemical.com...
Good luck with your Calamondin orange.