Hard to follow the storyline of what happened.
Three birds dead out of how many total?
Only 1 dead bird was locked up in an area into which entry could only be gained through a 2 inch hole? So somehow it was killed and eaten inside? The "eaten" part could easily be rats, but would they kill it too? How big was this bird? If a young bird, rats might have killed it too. Or your weasel/stoat or some such, but normally they will kill all, or almost all, birds in the flock. They don't eat much, however. So the eating part may very well be rats. The killing part prior to that.....hard to say. If you only had 2 or 3, a fox might have gotten one of them, stoats killed the others and rats did the eating?
Where was the bird that went missing and what time of day? A missing bird, no trace, could be a fox, if bird was out and about where a fox could get to it.
So you may have a lot going on, but from the information provided, it will be hard to say what.