I just bought a Duplex myself "House Hacked" in late 2015. I just remolded the side I was living in from top to bottom. new floors, paint, bathrooms, tile, doors, .. so on. If you plan to do it all yourself like I did. I would suggest that if you go with hardwood floors to go Click floors, they are extremely easy to put in and they look just as great!! Next (be Warned) If you go to war with your Bathroom it will fight back. The one place I ran into the most issues was the bathroom. Keep in mind it was nothing painful just gets frustrating when the old piping doesn't fit and you have to make 5 trips to home depot. I have now learned the hard way of how to avoid this going forward.
If I was to do it over, the only thing I would change would be (Nothing) It has come out great through the ups and down, and was a great learning experience. I would suggest finding someone who has done things before so you can nitpick their brain for knowledge and tips.
Good LUCK!