I just got back from riding a modified version of the south loop - The main route is all easily rideable, but the info that I received from other riders is that high elevations of the singletrack sections still have some snow making things difficult - I personally encountered snow at 7800 feet.
Also, based on my experience, I would highly recommend not riding the Lowman cutoff on a Sunday, the traffic is pretty heavy and moving fast trying to get home to Boise. I personally witnessed a motor vehicle collision along the way due to careless driving. I think that riders would be wise to consider riding the slightly longer Bear Valley Road instead to avoid traffic (I wish that I had - even though it does skip the Sourdough Lodge): https://goo.gl/ygYrMq
Caveat: I did not ride this alternate route, so I don't know for sure what the riding conditions are along it, but if the other roads on the route are any indication it would be a nice ride.
If anyone is interested in a doable shortcut to skip Ketchum (my time was limited so I crossed the Smoky Mountains from the South Fork of the Boise River to Smiley Creek), here is my tracklog: https://app.strava.com/activities/332753823
The hike up over the Emma Creek/Smiley Creek pass is not really rideable until you crest the pass going eastward, it's a hiking path with some rideable sections, but it is hike-a-bike-able with no major obstructions and shortens your route by a day or two.
For people who are flying in with bike boxes, I stayed at the super 8 by the airport on my first and last nights, and they stored my box for me in the interim - your mileage may vary, call to verify that they will do the same for you.
Edit: Also, for anyone riding the Bogus Basin cutoff to get back to Boise, water is nonexistent after Harris Creek - fill up before you start climbing or you'll be in for a rough ride.