First off, welcome to the site. Looks like you joined in February '16 so make sure to go to the new member thread (here's the link) and introduce yourself:
http://www.cvoharley.com/smf/index.php?board=30.0Now, you can lower your bike removing the stock air shocks and installing the short version of the HD Premium shocks. The ride will GREATLY improve over the stock air
rocks shocks. Best thing they did for the '17s were to finally do away with those dang air shocks. Yes, you can spend much more money on Progressive or Ohlins and they do ride great. However, you can find a good almost new pair of the HD premium shocks for $300 to $400 bucks. If you end up not liking them, you can resell them and get something else. I ended up purchasing from a member on the site for $350 shipped...very good investment.
The HD premium are very good shocks. I found the ride much more controlled with them. They came stock on my '12 SESG and I replaced the air shocks on my '15 SERGU with the shorter set of HD premium. Rides better, I ride single, two up and with luggage all the time. No bumpy riding. Actually I found even though they were a bit shorter (it works out to just over 3/4" shorter than the stock air shocks) they took the bumps much better with no bottoming out. I do have them a bit firmer than the manual states but I enjoy it that way. Your wife will notice a much better ride and you will enjoy the bike both as a single rider and with your spouse.
As for being 5'9" and can't touch flat footed? Something is off there. I'm 5'6" and could stand flat footed on my '15 with the stock air shocks (with boots on....and not elevator shoes, either...

) and stock seat. Yes it was a stretch but both feet flat. However, when I lowered it with the premium shocks, it did give me a bit more elbow room on the flat foot department so they should be great for you.
Good luck in whatever direction you go and keep us posted.