Good news! Tomorrow is my last PT session, so they told me to try running this week. If I don't have pain then I'm considered cured and released.
I went out and did the first week of Couch to 5K and it was wonderfully pain free. I guess I'd never noticed how bad it had gotten. When I first went in to the run intervals I actually cringed waiting for it to hurt. I had gotten used to the idea that running was going to hurt my knees the entire time I was doing it. Getting through the entire half hour without pain was nice to say the least.
I'm a little down about how much I've lost after not running since November... but it will come back. Just this time I'm going to take it a lot slower.