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I made a little script for you that will do just this. You currently have to paste the html for the tables in question into the HTML window, but after you do that just hit Run and you will see the combined tables. If you would like something more advanced, please let me know.
I would try just using plain old microsoft word, and zoom out to a point where you can see both copies on the same screen. Then they can be printed on different sheets, and comments can be added as needed on microsoft word. If you need to use an online tool then there is google docs word, but then you can't see both at once.
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