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I wrote about phantom pain for my web paper:

"20% of [individiauls born without limbs] experience phantom sensations (1). For instance, K. Poeck’s 1964 case study described an 11-year-old girl born without both of her arms. Remarkably, the subject learned to solve simple arithmetic problem by counting on her phantom fingers. Similarly, V. Ramachandran reported similar phenomena in his 1993 study; his report described a 20-year-old female who displayed congenital limb deficiency, yet experienced very vivid phantom limbs that often gesticulated during conversation."

Given this piece of information, it seems to me that abberent nerve-ending growth on the most distal portion of the "limb stump" is not likely to be the cause of phantom limb pain in individuals who havn't experienced life with limbs. Rather, perhaps the root of body phantoms lies in the brain.

1. Central mechanisms in phantom limb perception: The past, present and future