You might have a problem with the construction skills. I don't think there is a way to train builders once you have finished all of the construction projects. That ability has been requested and might make the update when it's released.
The boulder puzzle depends upon certain levels of research AND a special event. Patience is required.
Your scientists will usually abandon the research table once all tech levels are maxed out.
The key to the 'dead flower' field is somewhere else on the map. Why don't you try to explore things a bit with some of your villagers?