I have one early and one late door for my car. Do I need a matching set to seal to top?

Yes.

To expand on that a bit, if the door doesn't match the top and seal, it will leak.

Here is a classic thread showing the differences between early and late tops:
http://www.914world.com/bbs2/index.php?showtopic=73129

Ok. So I have one early and one late top as well. Looks like I need to get a driver's side late door. Thanks Andy.

Interesting,
I know the WAS tops, which were molded on the late style were interchangeable for early or late cars. So the top seal really should be about the same. There is a different end cap on the door that is slightly different in height. The doors have the same physical dimensions, it would seem that you should be able to address with seals.

Hit me up and I'll send you the seals if you post your results here.
-mark

It will be awhile before I fit the doors back on. I was looking ahead, did not want to paint the car with wrong doors if they don't work with the top. This all started when I found an inch of Bondo on my early passenger door and replaced it with a late door.

In reality, I may never drive with the top on or in the rain with this car.

Nope, the seals have a different shape and are mounted slightly different.

The later seals have a distinct "lip" and the top of the window slides into that lip.
Earlier seals do not have that and relay on a perfect alignment of the top glass to seal correctly.