Allow me to interject here. My simple response is this: if your goal is proper English, all three are wrong, but for a reason completely unrelated to the other respondents' answers above.
- They are shorter than me and lean
They are shorter than me and lean
They are shorter than me and are lean
They are shorter than me and they are lean
- They are shorter than me and are lean
- They are shorter than me and they are lean
In all three, "than me" is perhaps considered "colloquial," but it's not perfect. Instead of "than me," each should say "than I." Sure, lazy or modern grammarians may argue that "than" is a preposition (which precedes an object) and that treating it as a conjunction is elitist, pretentious, or some such thing.
But when professionalism and grammar skills matter, such as in court or in a prestigious publication, don't settle for the "'than' is a preposition" argument. At a minimum, use the subjective form plus the implied verb—e.g. say "than I am" instead of "than I" if you are concerned about sounding too proper.
Let me give you another reason to start doing things as I'm recommending. Take a look at this modified version of your sentence:
John likes short, lean women more than me.
John likes short, lean women more than I.
Now hopefully you agree these two have completely different meanings. In the first sentence, John is more attracted to short, lean women than he is attracted to the speaker. In the second sentence, the speaker doesn't like short, lean women as much as John does. If you don't see this yet, look at the following repeat statements that also include the optional, implied parts in brackets:
John likes short, lean women more than [he likes] me.
John likes short, lean women more than I [like short, lean women].
So if we accept that there is a difference in meaning here, why should we allow "than me" to be functionally equivalent to "than I" in any other situation?
Now let's revise your original statements. You should now see more easily which one is the best choice (the bracketed verbs are the implied verbs that can optionally be included):
- They are shorter than I [am] and lean
They are shorter than I [am] and lean
They are shorter than I [am] and are lean
They are shorter than I [am] and they are lean
- They are shorter than I [am] and are lean
- They are shorter than I [am] and they are lean
No. 1 is wrong because I cannot definitively (absent your providing alternate choices) determine whether "lean" is an adjective or a verb. "Lean" as an adjective is not the same as "lean" as a verb.
No. 2 is fine—definitely an improvement over no. 1.
No. 3 is best. I prefer this one over no. 2 because it more cleanly separates the comparison between what "they" are and what "I" am from a logically separate statement describing only what "they" are.