The door seals on my '99 Miata were torn at the tops of the triangular door glass, allowing water to leak in. Apparently this is not uncommon, but needed to be repaired in any case. My friendly Mazda dealer ordered both the right and left sides for me at a cost of $69 each. Part #NC10-58-760F for the right side and NC10-59-760F for the left side. Here's how the old and the new look side by side, and the new seals. As you can see form the unwrapped seal, these go all the way around the door in one piece so be careful not to tear these when handling them.
I started by removing the interior door panels, position the window about 1/2 way up/down. My car has modified '01 panels so I will not detail how they were removed as my procedure will not apply to any other Miata. Once the interior panel is off, you will also want to remove the inner plastic liner. As I pulled the plastic off, I ran a single edge razor blade along the black goo line, cutting the black goo so that it didn't stretch out and get all over everything. Trust me, whoever does your laundry will not be happy with you if you get this sticky tar all over you. Lay the plastic sheet aside, but pick a place where your neighbor's cat won't walk on it and track strings of black goo all over your garage floor....grr...don't ask. Then remove that metal panel in the door (3 phillips screws) so that you'll be able to reach inside the door to pull the new seal into place later.
Now you can remove the old weather seal, keep the window about 1/2 way up/down. Start at the back of the door. When removing the seal, you'll need to be careful at the top edge of the back of the door, the single pin on the back side is part of the exterior window trim and you don't want to break it. Otherwise just pull the pins out and start pulling the weather strip off as you go around under the door. No need to worry about the pins as the new strip has them already installed.
As you come up the front of the door, you'll come to another place where you'll need to be careful. This is right at the base of the triangular window where another pin from the exterior window trim must be saved. Then pull the seal out of the metal track along the front edge of the triangular window. At the top you'll find a phillips screw that needs to be removed and saved for reuse. The remainder of the seal that runs down the window track can now be pulled up and out, unless the track and weather strip have somehow fused, there is no need to remove the window glass to remove the old seal or to install the new seal. As long as you now have the weather strip out of the way you can go back and pull out those plastic pins, clean out the crud that's accumulated under it over the years, fix any rust, etc..
The Mazda shop manual seemed to imply that the window needed to be removed to install the weather strip, I figured that if I greased up the weather seal with silicone I could get it to slide down the metal track and along the front edge of the window if I was careful. I used a generous amount of silicone and this worked out just fine for me. I lubed both the outside of the weather strip where it would fit into the metal track, and the inside where the window would slide. Then I started by sliding the new seal down the metal window track, being careful to not damage it as I slid it between the metal track and the window, until it was about halfway down and wouldn't slide any more.
Once the weather strip was about halfway in I was able to run the window all the way up and reach inside the door (watch that black gooey tar crud) and slowly pull the weather strip on down until it was in it's proper position.
It'll take a bit of wiggling to get the top corner in position and tightly fitted around everything, but once you've got the corner back in position replace that screw. Watch that you get the rubber blocks tucked back in at the front corner, but from here on this is the easy part... you're almost home!
Now all you need to do is run the weather strip on around the door, pushing the pins in place as you go. Before replacing that inner door panel, run the window up and down a few times to be sure that it's not binding and that all is working properly, then put the rest of the door back together and go for a ride. You did remember to plug the tweeter speaker back in, didn't you?