Ward;
Never had a problem getting the holes dead accurate, if the LE is straight the holes are all located from the front. If the trailing edge is the straight part the holes are located from the TE. Now if both are tapered just use the stack method and drill them all at once. In the case of the straight LE or TE, I make a simple "Jig " that is "L" shaped with a center line on it and clamp it to the drill press table.
As for the twisting when pulling the rods out, I have never seen it happen, so I couldn't tell you what went wrong there. I have been using my "Jig" for quite a while now with narry a mishap. The wing always comes out straight.
When doing the "Ringmaster 1000" wing I only used 1 rod. The spar acted as the other rod---No Problem.
"Billy G"