Sorry, I made a mistake regarding each secret. I had them mixed up...
The green gem is in Eastern Zhaoze and is accessible by
pulling the lever in the far east of Eastern Zhaoze. It is near the ratling and the "Greater than two, fewer than four..." clue. Pull the lever, then head to the area central-west that houses the sign "there's nowhere to run". Jump down the pit and solve the little puzzle. Once solved head back to the start of the puzzle and enter the newly activated teleporter. Finally, you'll be able to reach the green gem (which, again is not plot important).
Secrets are the harder puzzles to solve while the main puzzles are much simpler.
Oh, how could I have missed the lock in the Woodlands, I am so stupid! Thanks!
Yeah, it sucks about the locks. I have done that on many mods before.
