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Well, I am not sure what Acrobat is doing to your files, but I would suspect that if the html doesn't format it quite right, then the PDF isn't going to either, not unless it overrides the stylesheet that is used in the html file.
That being said, I recently downloaded princexml (just search on princexml) and I found it works rather well at converting html files into PDF's sized for the screen size of my reader. The biggest issue I had was that I had to set maximum height for the images so that the images would not over fill the page.
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Bill
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