(1) can never be correct because the present participle [waiting] cannot stand alone. if it's converted into [what you wait for], it can be correct in the following condition:
e.g. what you wait for is timing and luck. 你等待的正是時機和運氣
(2) is correct even it stands alone as a question. it has a complete sense when it alone stands. you can also twist it a little bit and make it as a clausal subject:
e.g. [what you are waiting for] is timing and luck. 你現在等待的正是時機和運氣
e.g. [what you are waiting for] is for the rain to stop 你在等待雨停下來.
it can also exist as a supplement:
e.g. This is exactly the bus [you are waiting for]. 那正是你要等的巴士.
e.g. He is not the man [you are waiting for]. 他不是你要等的那個男人.