how much time to visit each of the birds nest and the water cube (not sure if I'll do water cube)?

Well, 1.5-2h is enough for the Bird's Nest and 1-1.5h is fine for the Water Cube.

Walk from the temple to Yonghe Lama Monastery metro station and take line 5 to Datunlu East. Then change to line 15 to Olympic Green. Leave from exit F and walk to the stadium in 6-8min.