Thanks for your kind words!
Production doesn't occur when storage is full (or when bees are carrying enough of that resource to fill storage), but bees foraging for resources outside the hive will bring back whatever they find regardless of whether there's storage space or not.
Regarding difficulty, the game's balanced so that once you know the ins and outs of how the game's systems work, it's not too hard to get enough Jelly in half the provided time. As a "continue playing" condition, I wanted to make sure that it presented as a soft learning gate for new players while not presenting a significant hurdle for experienced players. If you haven't already, take a peek at the Bee Activity screen (accessible from the upgraded Throne Room). It can give some clues/cues for efficiency bottlenecks that might be slowing things down.