For the quest: 2 Stone, 2 Wood, 2 Soil and 2 Clay, and 300 S for completing the mission.Is there a better guide than the wiki that also shows how obtain the bonuses after every mission?
I don't know how to obtain Bonus 1 and Bonus 3 on Quest 3 "You must be registered to see the links."
But I suspect you are wondering about the map bonuses.
For the map (Sunlit Clearing):
100% completion (Bonus 1 - this is always bonus 1 task) 300 S. That one is impossible without a flying unit.
Bonus 3: Phoebus Stone. Either requires flying (which you don't have for a while) or killing the Harpua who might steal the treasure in the lower room. You will get some form of notification that that has happened. After the message just hog the lowermost room in the middle of the map, and kill it.
The Harpua does not always steal the treasure though.
For future reference, you can't always get all bonus tasks completed on a first playthrough the moment a map becomes accessible.
As for better information, on page 8 I posted an excel file with pretty comprehensive information (on October 12 2019). The alternative would be the Japanese wiki, but I suspect you can't read that (and if you have to rely on google translate it can become a nuisance).