Marshal:
There are probably a couple of answers to this, depending on what kind of data you're looking for.
If you just want a "quick and somewhat dirty" calculation for the Zin of the antenna elements, you can probably do this with a lumped port between the antenna elements, neglecting the twin lead fed entirely. This gives you a characterization for the antenna elements that neglects possible coupling to the twin lead feed. It probably runs faster and requires a smaller simulation volume, though.
If you want to include coupling between the twin lead feed and the antenna, but still want input feed characteristics for the antenna alone, you should use a wave port (which might be a little tricky to set up if your antenna has a lower physical ground plane), and set a de-embedding reference plane to the point where the twin-lead connects to the antenna. This gives you a Zin for the antenna that also takes into account the feed-to-antenna coupling, which might be significant.
Finally, if you want the effect of both the antenna and a prescribed feed length, I would suggest a wave port located at the lower end of your workspace so that you also include a proper amount of finite twin-lead feed. I don't know if you're working with a lower ground plane or not. If you are, use the design distance. If you don't use a lower ground plane (i.e., this is in free space) then you better model a sufficient distance to the lower absorbing boundary according to the vendor specifications for such surfaces. You don't want absorbing boundaries eating up field lines that are supposed to close in upon themselves in the model.
You could use a lumped port at the bottom between the leads, but this would add an additional discontinuity to your results that might add unacceptable error to yoru results at high frequencies. The wave port will start with the understanding that you already have a TEM mode propagating up your twin-lead line.
Make sure that you make your wave port large enough to capture all the feed lines. Be sure to check out the field lines in the port to make sure that you don't have too many of them terminating on the sides of your port surface; that would mean you need to make the port area larger.
Hope this helps.
--Max