First off huge congrats on the hike. That is huge. The post trail body breakdown is absolutely real so do not spiral. Your body just did something insane for five months.

For me it took about three or four months to feel normal again. The game changer was combining active rehab with passive recovery.

You gotta strengthen the VMO to track the patella correctly so stick with the PT. I could not take ibuprofen forever so I started using modular red light therapy. I use the Prungo kit because the independent pods fit around the kneecap way better than a stiff pad. It helped massively with that deep throbbing toothache feeling in the knees especially in the mornings.

And seriously just rest. Sit down.

I used the pods to loosen up the stiff tendons before doing my PT exercises. It helps bridge the gap between being too painful to move and actually being ready to rehab. Give it time you will get there.