Thanks for writing in,
If you develop any swelling in the joint along with any difficulty in running or jogging, then it is advisable to get yourself examined by your doctor. You can use knee cap while doing your activities.
The small pea sized lump under the surgical scar might be the end of hamstring
graft. It is usually felt after all ACL reconstruction. Nothing to worry about it.
If the cracking sound is really bothersome with/ without swelling / pain, its better you get your knee examined by your doctor.
Wish you a good health.