Well, here is another update.
Turns out the majority of the pain was coming from Hoffa Fat Pad Impingement Syndrome. A torn portion of the fatty pad under the patellar tendon becomes inflamed and pinched causing crazy pain. That has since subsided, however, the torn tendon is still an issue. I've completed physical therapy, and I still have a pretty constant mild pain. I have full ROM and full strength (though some things cause more pain than others). My surgeon has stated that I should try living with the pain until it becomes unbearable, as she doesn't recommend the surgery yet. My plan is to keep working out and exercising (and riding) over the summer, and just biting the bullet on surgery after this season.
Currently to ride, I have to wear a patellar strap and a brace. Kind of ridiculous that nothing can be done at this point and I am extremely frustrated. I just need to wait now I guess.