When you have a page-template file, delete it. Then in each XML file, delete the reference to it. Also delete the reference to it in the OPF file. I use notepad++ and this makes it very easy to handle this for however many XML files there are.
As for the CSS, deleting it is a rather bad idea. Take the CSS and edit it to make the ePub look how you want it to look. That way, you won't lose things like italics, bold, font sizes and other things. You will have to look in the XML files to see what CSS entries you may want to edit. I do this a lot and overall, it's not difficult to do.
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