SOBO entry to JMT at MTR

Hiked Happy Isles to MTR in 2016 but had to exit via Florence Lake as hiking partner encountered excruciating pain in her knees. Turned out to be stress fractures in both tibia. Wed like to finish but are uncertain on how to go about permiting for an entry at MTR. I considered putting in for a permit for the whole trail again but that isn't what we really need and it would, if we were to get one, cheat someone else out of entry in Yosemite. Any insights into this would be greatly appreciated. Jim