I also used Polk Audio dxi6500 components up front and added an amp. I still wasn't completely satisfied with the sound, and used VagCom/VCDS to change the settings to external amp.
To do it over again, I might have just tried replacing the tweeters. The stock woofers don't seem so bad, although they are awfully "boomy" in some frequencies, which the stock amp probably compensates for. Anyway, the only stock crossover is probably the capacitor on the tweeters.
To help with the rattling door, I put dynamat on the big flat areas of plastic. While I'm sure it helps, it still distorts some.
Without an amp, the speakers just didn't sound quite right. You don't need a big amp, just a decent one.
I keep thinking I should put up some photos of what I did. (It will take some time...)
By the way, consider that you may need to use VCDS for some audio changes, as it has a setting for monitoring the tweeters, for example. Factor that cost into your plans...... $$$