OK so you left the shifters at the bottom. I can see why you recommend going with cables. I don't think I've seen anyone do a flip and not relocate the shifters. Seems strange that others aren't doing it. How far did you have to clock it so the shift rail wasn't under the yoke?
Looks like AA sells a cable kit for their Atlas; http://www.4x4groupbuy.com/store/advance-adapters-atlas-cable-shifters-p-4754.html
There's also these: http://www.northwestfab.com/Dana-300_c_82.html by the description, they recommend using the reverse kit which has the longer lines even in a flip situation? Seems that would be too long unless you're using a doubler.
Others have done it, there's a guy selling the flip shifters (to use it as i installed it) on ebay, i looked at them way back when but decided will make my own, with his you would use the stock mountpoint for the shifters and i think you would have to keep it clocked more (but i'm not sure) - problem is that most of them have leaks since they keep the old rails and like me initially use the omix replacement seals which are extremely sucky, i can give you the part number for the other ones if you ever get to that point, they don't leak a bit but like i said I got brand new rails. The other thing i forgot to mention is that you need to modify the front shifter rail to allow for 2wd-hi/lo-front/rear.
mine was initially clocked 15 deg, but after the doubler install is only clocked about 5 or so. If you go by center shaft to center shaft is pretty much horizontal (look at the pic below between the rear output shaft and the cap for the front output and you'll see what i mean, the bottom is angled a bit more than the actual centers of the yoke shafts). I've had no issues shifting to hi/lo either front or rear. the shifters rods are positioned much better now and it aint touching anywhere (tested the driveshaft and is not even close.
the pic you posted is in the new clocking position, it was much worse before, it's aligned fairly well with about 1'' offset.
here's a better one with it installed in the jeep