During the root regeneration phase that follows transplanting a young tree, do not prune the top of the tree. Pruning at this point only serves to remove leave area and slow down root growth. A pecan trees will tell you when they are ready to be trained. Two to three years after transplanting, the top of the tree will suddenly explode with new shoot growth (especially with proper weed control and adequate soil nutrition). This is the tree's signal that the root system has become well established and the tree is ready to be trained.
Training a young tree that grows rapidly is relatively easy using the 2 foot rule. It just requires paying attention to details and a monthly inspection (and pruning when necessary) of your trees from May thru July.
The last post in the training young trees series is Summing up