I've talked at length about training young trees in previous posts. Almost all of the mistakes growers make in training young trees are related to a lack of appreciation for a pecan tree's natural growth patterns. Lets look at some examples.
narrow angled crotch between the two forks of the tree is inherently weak and subject to breakage. Sure, correcting this problem is easy--just use a chainsaw to remove one on the two leaders. However, waiting to correct this problem until this point in a tree's life will result in removing one half of the canopy and 1/2 of next year's nut crop.
Sun scald has the potential to kill the trunk's cambium on the exposed side of the tree and slow trunk diameter growth.
Lower limbs need to be removed slowly, over time. My rule of thumb is to never remove more than two lower limbs per year.
For detailed instructions for training young trees including "directive pruning" and the "two foot rule" read through my blog series starting here.