I have found the Competitive Cyclist fit calculator http://www.competitivecyclist.com/za/CC ... ATOR_INTRO
to be pretty helpful in setting the position in the right area, then tinkering from there! It certainly set me up pretty well, just a few small details to tweek and I'm happy.
Saddle to bar drop will be different than on the road. Especially on the 29er, unless you are riding an XL frame, as the big wheels raise the front end up pretty high. You will run less drop, but a lot of it will depend on what style of riding you are doing, if it's XC racing you will have a lot more than generic trail riding.
I think mine is currently about 4 inches, compared to nearly 9 on the road bike. However, that is on a 26er hardtail, that might be reduced to 2-3 inches on a 29er unless I switched to a -17 degree stem or something similar.