Don't bother with the MPLAB if you are just trying to write to a few chips. Just use the pickit3 Stand Alone Programmer from this link. I had the same problems last night and got mine working great after doing a little research.
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LoginOnce you install and load the program, you are likely to notice that none of the dropdown menus work. If that is the case, click Tools ->Download Operating System as described in this previous thread. Install the .jam file.
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LoginAt that point the pickit dongle should show a blue light as it is being updated. The status window will indate that it's finished, but green bar on the pickit screen never quits it "updating loop". Not to worry, your pickit is now ready to use. As you use the dropdown to specify your chip, it will automatically install more updates as needed.
Good Luck,
Mike E.