Other things to explore if you haven't alreday is McConnell taping for the knee. Your PT can show you how to do it. I tape my patients and leave the tape on for up to 2 days to allow the tape to help stretch out the soft tissue that affect the patellar alignment. I also teach patient how to do the taping prior to activity to minimize pain during the activity.
Yoga is very helpful too.
And don't forget to look into trigger point dry needling if you can. It has helped me a great deal with my own chronic patellar pain (related to thigh and hip issues).
I feel like I'm bombarding you with stuff, but really it would be so great if you could find a solution without surgery being necessary.
Good luck.
Living life like there's no tomorrow.
http://gorgebikefitter.com/
2007 Look Dura Ace
2010 Custom Tonic cross with discs, SRAM
2012 Moots YBB 2 x 10 Shimano XTR
2014 Soma B-Side SS