Find an extra chunk of door seal, a foot or so will do. You can get this from a junk yard or from another car even. You can also buy seals but they are expensive. I took a piece out of a a minivan that is used as a parts car. The best one to get is one that matches your car. If you can't get that then try and get one that is a close match. Door seals can be difficult to cut because of the metal pieces in it. I used a pair of tin snips to cut mine. Really heavy duty scissors might work also. A knife will only cut the rubber. A hack saw will work but its a little more effort.
After you get your seal material figure out how much to cut to fill the gap. First make sure the seal is pushed completely into the door frame. Next mark on your chunk of seal where to cut. Make it BIGGER than the gap by about a half inch. This way when you put it in place it will push against the rest of the door seal and help to force it to stay in place.
Push the piece you cut into the gap and hammer it down with your hand. You should not have to do it very hard. It goes in pretty easily. You don't need to use any type of glue since the pressure will and the sill cover will keep it in place.
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