I am going to first state that the knee and knee related issues are often complex, and two very similar symptoms can have vastly different causes. You should really be seen by a professional sports med doctor, physiotherapist, orthopedist, or similar – preferably with experience treating cyclists.
That said – I had my first bout of knee pain, which led to a significant knee injury, after raising my saddle. Raising the saddle wasn’t the cause, it was mostly the ‘final hair that broke the camel’s back’. In my case, the cause is/was imbalance that was mostly attributed to having a sedentary desk job, and getting heavily back into cycling after a decade off. My ‘bike quads’ developed, but my hips, glutes, etc all fell quite far behind, leading to a patellar tracking issue from a ‘tight’ IT band (aka patellofemoral pain disorder).
The IT band is rarely the issue though, it’s the relative weakness and instability of all the other muscles that allow the tighter IT band to pull the patella out of its track, which wears down or irritates cartilage and surrounding tissues, hence the pain. And when taken to extremes, the wear/tear can cause permanent damage to the joint. So, it’s really hard to say what the problem is without an actual professional taking a look
My unprofessional suggestion would be to get it looked at, but also probably revert your saddle change, if not completely then just somewhat. In particular, moving the saddle up and back will change your torso angle (‘more aggressive’), tightening up you posterior chain, which will cause more tension on your IT band, pulling the knee more.
One of the things my physical therapist did was move my saddle forward some, and raise my bars via +1 cm spacer to ‘open up’ my position, taking some tightness out of the posterior chain while I strengthened the glutes/hips through targeted therapy. In addition, my stance was widened a bit by moving cleats inward, and adding a couple mm of spacer washers to my pedals, and I was told to focus on keeping knee vertical. Allowing the knee to track inward on the downstroke adds more tension to the tendons, pulling the patella over more.
Anyway, this is a lot of specific details about my scenario, but hopefully its helpful information. Most important thing is to get it checked out by someone who really knows this stuff before long term damage occurs.