Why was the Professor so upset when he awoke after the first night in the crater to a cloudy sky? When and how did they finally get the indication of which direction they were to go? 

The clouds delayed the journey, and the Professor knew that is the clouds hung over them for another six days, their journey would have to be postponed for another year.

If the kindly heavens would only remain densely clouded for six more days, we should have to put off our voyage of discovery for another year, when certainly there would be one person fewer in the party.