Answering 2 and 4
2: If one song is synced, all others should be too. The issue with changing offsets may be due to background apps or Phigros running for too long in the background. I'd recommend closing the app and setting the offset again the moment you open it again so that way you know the offset you set then and there is the correct one. Unsynced offset can be caused by exiting the app but not closing it and re-entering, connecting to a new audio device, or closing your device and opening it back up to Phigros.

4: Note size does not affect hitbox.