What are you saying stinks?
makes perfect sense.
To understand it easier, you can convert it into a declarative statement:
You are saying something stinks.
Here, "something" takes place of the interrogative "what". If the sentence is still a bit awkward, then perhaps add a conjunction:
You are saying that something stinks.
To make an interrogative statement out of that (about 'something'), you change "something" back to "what", move it to the beginning, then reverse the subject-predicate pair:
What are you saying that stinks?
As you can see the only difference with the original question is the "that", which we put in front of "stinks". Its position is not obvious, although does become clear once you perform that mental juggling.