Hi, I called Matt at Hobie and he says the harken furler does have the shackle on the top and that the drum is inverted, (harken logo down), but he said I could put another larger shackle on the bottom, since the one that is on top now is too narrow, so the furler is logo up.
When I said shaved I meant to say the shaft is ground down a little on two sides so the shackle fits, Matt said the ground down area would not affect anything, but I am not going to grind the other shaft down. I will get a bow shackle that will fit, (instead of a D shackle, which is on it now), so I won't have to grind down the sides of the shaft, that way it will be set up like your's, which makes more sense.
So I guess I will have to go to St. Louis to pick up a larger bow shackle and make sure everything fits right,
Hopefully I will get to sail sometime this summer!

Thanks for all the help! The photo helped me a lot!