I am also struggling with this at the moment (have been since Christmas). My research and NHS physio suggest muscle imbalance causing patellafemoral pain syndrome (and it came on about a month after taking up single speeding funnily enough!)
I think I am finally on the mend now (managed to be pain free after a ride on Tuesday night!). Things I have been doing are:
1. Complete rest from the bike until I have been pain free for a week to let the inflammation go down a bit (this is the hardest part)
2. Stretches – especially quad, hamstring, IT band, glutes, hips, calf, hip flexors
3. VMO – plenty to try but my favourite has been the leg extensions in the gym using the machine. Just doing the top 20 degrees and feeling that I am pulling the weight up just by contracting my VMO.
4. Hip abductor – (weak VMO is likely from an alignment issue triggered from the hips or the ankles) – side leg lifts, side knee lifts and dropping/raising one side of pelvis while on a step
5. Leg/knee stability – This brings all the above together. Single leg squats with a real focus on knee tracking (at first mine would point inwards very easily despite being able to do the squats without issue)
6. Foam roller/sports massage on IT band and outer quad to loosen off any pressure pulling the knee cap over.
While riding I have been avoiding winter bibs as they put pressure on the knee cap and can affect its tracking slightly, focussing on my knee tracking while pedalling (especially out of the saddle) and then doing a full compliment of stretches, foam roller and ice pack on the knee after.