nutnut4,
The large amount of callus (a golf ball of bone around the break) is very normal, especially in fractures that have had on infection in them.
It is concerning that you are having an increase in pain at the fracture site, after a period of doing so well.
A recurrence, or an indolent, infection is always a concern, though it has been a very long time. So, this is low on the list, but has to be ruled out.
Removal of the intramedullary (IM) nail probably would not take your pain away. It is always an option, if the bone is completely healed (without any infection). But, it is another operation. The incision at the knee would have to be reopened, the end of the nail found, and then hammered out of the bone. Again, it probably would not take your pain way, but would be an option, if nothing else helps.
But, since your are having a significant increase in your pain, after a period of great activity (being able to run, etc), you need to see your orthopedic surgeon for an evaluation.
Some new x-rays and maybe some labs need to be done.
Hope that it is not something serious, and that you can get back to your activities.
Good luck.