Wil,
I've been involved in a couple of shoring projects for large transport aircraft and I feel your pain. There isn't much in the way of reference material for the engineer.
A lot of the design is done by using "best shop practices". We tell them where to support the aircraft, and the shop just figures it out. Depending on the kind of work you are doing (how much you can allow things to shift during maintenance) your shoring might be as tight as every one or two frames (or ribs), or as loose as every 5 or 6.
One big thing to watch out for is overhanging (or sagging) moments. Make sure that your aft-most (or outboard-most) shorings are sufficiently far out to prevent a large moment that will cause structure to "spring" when it is disassembled, making reassembly nearly impossible. One SRM shoring procedure I reviewed would have resulted in a 2,000,000 in-lb. moment from the empennage since the aft-most shoring was forward of the CG of the horizontal and vertical tails.
Here are some of the things we've done in the past:
Contour tolerances aren't that big of a deal; that's why you use some neoprene rubber or dense closed-cell foam to redistribute load over the hot spots. I think we generally used the neoprene in 1/2" or 3/4" thickness, mostly because we couldn't use the foam anymore after our "hot wire" cutting was disallowed due to toxic off-gassing.
Commercial-grade 3/4" plywood is most often used, and doubled-up as necessary. A thinner, 1/8" or 1/4" piece may be contoured over and around the 3/4" in order to create a base to attach the rubber.
Fuselage forms are generally placed under the frames, and wing forms are placed under the ribs. Try to keep the width of the forms equal to the width of the frames/ribs since you don't want to put big out-of-plane loads on the surrounding skin. Make sure the structure can handle whatever load you apply - basic weight and balance information is usually sufficient to approximate your beam over multiple simple-supports.
For welded structures, my favorite reference is "Design of Welded Structures" by Omer Blodgett. It's a GREAT book. You can find it on Amazon.com or other resellers.
Steel plate is generally A36 steel, and tubing is generally A500. These are both very mild steel and very easily weldable. (Also cheap and available.)
I have some limited design information on allowables in wood structures, if you can figure out a way for me to get it to you. It's in .pdf format. Don't post an email though - the Eng-Tips gods frown upon that.
Hope that's helpful.
SuperStress