redfish,
The boots are a tight fit by design so a bit of tubbing/pulling is in order to get them to fit. Try seating a rack of four carbs onto an engine. That can get ugly if you let it.
The boots on the airbox side are quite flexible in the horizontal direction so the in/out motion won't unseat them during normal use. Think sideways 'U'. There is a retaining ring around a flange on the airbox side so there's no chance they'll come loose from the box. The detachment was due to the carbs being forced back in a 'not straight' alignment. Don't be afraid to tug on them.
Using grease to help the boots back on wouldn't be ill-advised. But whatever you do DON'T glue them on! (ask me how I know this

) Rubbing alcohol makes a good short-term lubricant also. Needle-noses pliers are a good friend to have too.
Hope this helps.