Have a look at SilverFast (https://www.silverfast.com). It is dedicated scanning software that can do colour correction, dust & scratch cleanup, etc

I have found the Chrome extension from PrintWhatYouLike.com works well, allows you to remove all the junk you don't want and then save to PDF. Does a decent job in Chrome. Unfortunatley it does not work well in FireFox, which only supports a bookmarklet. They also have an extension/bookmarklet that can combine pages where you need to keep clicking "next" to see more content, into one single page. But I have not used that one.