Hashfield,
From reading your post, it sounds like you have two problems, (1) the speaker won't fit in the stock speaker bracket (2) the speaker is too deep, so the window hits the back of the speaker. You just committed the big mistake of buying your speakers without making sure they would fit the doors. If anyone else reads this post and is thinking of buying speakers, buy speakers that fit the doors!
Now the first problem is the easier of the two. Follow everyone else's advice and cut the plastic speaker bracket/enclosure. But my tip is to use a razor and/or dremel to cut as little off as possible. The reason I say cut as little as possible to make it fit is because the plastic speaker bracket/enclosure protects the speaker from water/moisture in the door. Tip #2, get a replacement set of plastic speaker brackets from the jy before you cut the plastic speaker bracket, since the dealer charges an arm and a leg for them. Now if you ever change speakers in the future and need the old plastic speaker brackets back, you have them.
The second problem is not easy. If you install "spacers" (something to eat up the space you need to clear the window), the plastic cover that screws on over the speaker will look raised (not flush with the rest of the door panel). The result is a cheap, ghetto look that will be a constant eye-sore, but it won't interfere with the windows. Surprisingly, this is your best solution (unless you want to ditch you speakers for speakers that fit, which is the best solution).
Or you can create custom door panels from fiberglass to fit your speakers, but the custom door panel would be more expensive than new speaker to have custom made for you. And making them yourself is a PITA. Not a good option IMO.
Or you can weld something to stop the window from moving down past the speaker. I have seen this mod suggested before in car audio forums, but you won't be able to roll the windows down completely. A really ghetto, lame solution IMO.
So make a choice and let us know how everything turns out.
If it were me, I would RMA the speakers, pay the restocking fee, and get speakers that are shallow enough so the windows do not hit the speakers. I went the ghetto approach and cut the plastic speaker COVERs on my old '87 Civic. It looked terrible and I always regretted it. And the plastics cover replacements from Honda wereoutrageously expensive, so I lived with it until I donated the car. I made sure the speakers fit my 3g, and I am a happy camper.
Peace.
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