I was surprised how well the factory furling kit works. Not as smooth and refined as my TI, of course, but still not bad. (I am using it on a '13 Outback as well.)
I took the balls off. I found in order to fully furl/unfurl the sail I had to move the lines much farther than the balls would allow - besides, one was backward as you noted. I'm used to just pulling on the rope for furling anyway so no biggie to me.
I also attached the bungee to the storage area loop. I've used the sail several times (only had it a couple months) and no problems at all so far. It does mean the lines stay on top of the kayak instead of running along the side, but I think I prefer that anyway.
I've found that the knot in the furling line needs to be positioned properly in order to get full furling ability. If I have it up near the fairlead when furled, it will go through the ring on the bungee and back up about 1/4-1/3 of the way toward the fairlead before the sail is fully unfurled. The rope does slip a bit on the furler from time to time but it's easy to reposition as needed.
I put a (cheap, laying around handy) pulley on the stern padeye for the mainsheet, definitely helps. Still need to put a turning block up front and add a cleat. Keeping the sheet in my hand the whole time is cramp-inducing after a while, especially in heavier winds!