It seems most of the MTB world starts with 32x16 or 17 as a baseline gear to try. I am building an SS 29er and am wondering what a good starting place for the larger wheelset would be?

You are right, 2:1 is the usual starting place for 26 inch MTB's (32x16 or 34x17 being common). If you want to get an equivalent gear, I believe someone told me you want to gear about 20% lower. Check Sheldon Brown's website for a gear calculator and you can figure it out exactly. I've ridden my 700c fixed gear Crosscheck (damn near a 29er) on singletrack using a 2:1. It was harder, but not enough to worry about since it's not my regular off-road machine.

Use gear-inches to compare the gearing. You have to take into account the diameter of the outer edge. Normal 700c wheels are 27" diam. Just fit 29" into the gear-inch equation.
gear inches= (#front teeth/#rear teeth) x wheel diam