Are you using an image editor to print? If not, then give that a go. 72ppi is pixels per inch. It shouldn't matter what resolution you use. Almost all modern image editors will understand this and print accordingly, as long as the fit-to-page or scale options are unchecked.
To fix your holes, it might be easier to cut out that 4x4 square and then glue in some scrap. If you go this route, then make the scrap just a tad bigger than the hole so that that you can hand-sand it to flt like a glove.