Here is a write-up with pictures on how to replace the front targa seal (a new targa seal is about $50). You accept all responsibility for any damage caused by following these directions! Enjoy!
Step 1: remove both A-pillars. You can just pull off the driver’s side a-pillar as it is held on by two pins. The passenger side a-pillar is held on by two screws and a pin. To get to the two screws, you have to take off the handle. To get the handle off, pull back the rubber on the top side and you will see a metal tab (you can pull the rubber back without tearing it, but even if it does tear it won’t matter) (see picture). Use a small, flat-head screwdriver to pull back the tab and slide the top part of the handle upward to take it off the clip (see picture). Once the handle is off, take out the two screws and pull off the a-pillar (see picture).
Step 2: remove the dome light, visors, and visor holders in order to remove the upper panel. The visors and visor holders just unscrew (see pictures). Once you take out the screw from each visor holder, they just pull out (use a flat-head screwdriver if you need to). To remove the dome light assembly, take off the clear plastic cover by slipping a flat-head screwdriver under the two tabs--this will expose two screws (see picture). Take them out, remove the dome light assembly, and the upper panel just pulls off (see picture).
Step 3: remove the two 10mm nuts on either side of the windshield that hold the old seal on (see picture).
Step 4: remove the three screws that hold on the wind deflector and pull the deflector off. You don’t want to strip these, so make sure you use the correct sized Phillips-head screwdriver. You may also want to use an electric screwdriver for the extra torque just to be safe (see picture). There is some sealant that forms a kind of washer on the back of each screw hole when you remove the deflector that you might want to reuse.
Step 5: On each end of the seal (near the front fenders) there are two small tabs. Just pull the seal off the tabs (see picture) and remove the tabs (the new seal comes with new ones). Now you just have to pull off the old seal—don’t worry if you damage it.
Step 6: remove any old sealant and then wipe off the entire area with rubbing alcohol or something else to clean it. You want to ensure the new sealant will adhere well to the surface.
Step 7: put on the new seal, starting at the top where the bolts are. Take off the plastic protecting the new sealant as you get to it. Work your way down the seal ensuring that the new sealant makes good contact. In between the corners of the windshield, there is a section of the seal that fits on top of a long metal tab (see picture). On both a-pillars, there are metal tracks (see picture). The seal has notches that fit into these tracks. Use a small flat-head screwdriver to ensure the notches go into the tracks correctly (see picture). At the bottom of each side of the seal, press the new plastic tabs (see picture) into the holes where the old tabs from step 5 went.
Step 8: now just do the steps in reverse to put everything back how it was. Make sure you put the visors on correctly or they won’t work right. To get the handle back on the passenger-side a-pillar, slip the bottom-half on first, then stretch the top-half on over the clip and ensure it snaps in.
I would like to thank Shitzu for sending me the basics on how to do this.
Edit: MKIII targa seal replacement pictures added below thanks to itsmeek.