I also have crepitus, and have also had knee pain of the type you describe. The crepitus started well before any knee pain, and has continued past when the knee pain disappeared. My doctor diagnosed mild chondromalacia, which causes the grinding noises, and said my cycling would help that.
I would personally avoid any high-force movements, especially including squatting, perhaps for two to three weeks. In my case, some aggressive plyometric work brought on some knee pain that went away after a few weeks of reduced-force exercise.
I would also work on ensuring that you have some measure of flexibility in the lateral quad and ITB on the affected side, but please make sure you don't mindlessly stretch it -- know what you are doing. Too much of the wrong type of stretching can be as bad as too little. Secondly, I would work on very light weight terminal knee extension exercises -- just the last 30% or so of ROM for that leg, using a 5- or 10-pound ankle weight, and focus on locking out the knee. This helps strengthen the VMO which in my opinion is much less developed by "straight cycling" relative to the strong lateral muscles in the quad. Remember -- heavier is NOT better for this exercise during any period of injury.
The point of the last two ideas is to balance the strength and flexibility of the muscles that pull on the kneecap and which can cause pain and related symptoms (chondromalacia). The idea is to gradually get the kneecap back to tracking properly.
Have you had your feet checked? Flat feet or overpronation can sometimes contribute to knee problems.
When you cycle, do your knees track straight up and down? Have this checked by someone standing in front of you on a trainer.
Again, these are all my opinions only. I'm not a doctor. Take it for what it's worth, and I hope you feel better.