I went and did some exploring tonight. It looks like the best way to run shuttle is the following:
Drive to Idaho City, go about 3 miles past Idaho City toward Lowman, turn right onto FR 327. Follow the road into the North Fork Boise River Valley. At this point you can decide whether you want to launch at Black Rock Campground or go upstream to the Bridge that crosses the river that's probably 5 miles upstream. Going to the bridge would give you a little longer run since the shuttle is REALLY long. At the bridge, you can decide whether you want to take the rough road (FR 376) approximately 7 miles over the hill to the Middle Fork Boise Valley, or the other choice is to take the car friendly route that probably adds another 10 gravel road miles to your shuttle one way. If you opt for the car route, continue on FR 327 upstream until you reach Swanholm Road (Still FR 327), turn right here. Go over the pass and drop into the Middle Fork Boise Valley. Then continue downstream to the takeout at the confluence of the Middle Fork and North Fork Boise Rivers. I really didn't keep track of the mileage but you can find the route on the Idaho Topo books.
Good luck and I hope this helps anyone considering the journey. The drive will likely eat up half your day or more to run full shuttle. I would recommend running shuttle the night before and putting on the next morning for a stress free run.