Hey Mack,
Thanks for reaching out with the question. Patellofemoral pain is a condition I typically see in the physical therapy setting. I know it can be frustrating but is definitely something that you can overcome.
Like you said, typically you will want to avoid movements that require your knee to travel over your toe. This just puts pressure on the patella and can be painful when it is irritated. You may actually be able to use bulgarian split squats as a substitute for step-ups and lunges as long as you make an effort to keep your knee behind your toe as you perform the movement. Additionally, you can perform box squat (just sitting back and down to a box at or a little above parallel). This allows you to sit back and place less pressure on the patella. If neither of these works when I would stick to hinge-based movements such as RDLs, KB swings, and single leg RDLs. This will work more of the hamstrings and glutes but is still a good way to help keep you moving. You can also perform movements to strengthen the hips such as banded side steps or fire hydrants in place of the step-ups or lunges.
If all else fails, then wall sits can be a great movement to still challenge the quads while reducing pain on the knee.
Let me know what you think of these suggestions.
Stay dangerous,
Coach Nick