I'm no Dr Butt:
For what it's worth, chondromalacia patellae (I gather it's also known as runner's knee) or patellofemoral syndrome is sometimes (often?) misdiagnosed as patella tendonitis because the pain is pretty much in exactly the same spot. This happened to me a long time ago.
Two physios misdiagnosed me, and a month of their recommended treatment did nothing (ice, rest and stretching), then the third guy got it right, and one simple exercise he gave me fixed me in less than a week. The simple exercise was straight leg-raises with very light weights. Were you told to do that exercise?
He diagnosed me by simply having my leg flat on his bench and pressing on my cap and rubbing it around. He felt roughness, hence his diagnosis of chondromalacia patellae.
Chondromalacia is caused by a dodgy tracking of the knee cap, resulting in the cap rubbing on the femur, which then results in grinding, roughness and eventually pain. I think it can happen for a few different reasons, but my physio said that mine was caused by a a misfiring of the quads, causing my cap not to get pulled up and out of the way of the femur quickly enough during knee flexion. So, tightening the middle quads fix it.
Twenty or so years on, it can still sneak back, but I still do as many kms as I like; I just do the straight leg-raises a couple of times a week as part of my routine.
I used to jog a fair bit back then, but that was the worst thing for it, so I'd recommend ditching running for a little while.
I quit running, because cycling was always my priority. A few years ago I jogged about 1km with my dog, and my knee flared up and bothered me on and off for a few months, so I doubt I'll ever jog again.
Other treatments for similar conditions -- chiefly patellofemoral syndrome -- basically involve trying to loosen all the outer stuff with stretching and rolling (lateralis, IT band, tibialis anterior, glutes and tensor fasciae latae), and trying to strengthen the medialis, which is very hard to do, because it's impossible to isolate, despite what some people say. In fact, according to many sites, it could be a myth that the medialis can be strengthened independently of the other quads.