Ok so this is my absolute favorite method.... I'd just need to make some (what i'd call) adapter plates to convert the strangely angled roof rails to a nice flat surface. Then, with the brackets extending about 1" below Doc's rack I'll have about 1/2" roof clearance (that I could increase or decrease by making some new adapters which would be relatively cheap and easy to machine).
Just need to hear from Doc on his thoughts about this idea and to work on a quick quote to see if its a path I can afford to pursue. If it looks good, we'll work on some more of the details such as actual dimensions and locations of the mounts.
Edit: And if I do go with this method, I'll be using socket head cap screws. That will help resolve any issues with bolt head (and tool) clearance with the rear mounts and look cleaner from ground level. Also makes it a little harder for someone to randomly remove since its a large hex size. May even look into some tamper resistant bolts...