How to fix my knackered knee

Hi, avid reader, but first post! I wondered if others would be able to share experiences regarding the ever popular subject of knee pain and injury recovery.
I’ve been road riding for a couple of years (mountain biking for much longer) managing a few century sportives without ill effects. In May this year, I was training for such a ride, and had started using a single speed track bike for a 12 mile each-way daily commute, aiming to increase the workload. After a couple of weeks I noted slight discomfort in my left knee. Stupidly ignoring this, I went on my regular Sunday morning jaunt (40 miles) but 30 miles in I felt sharp pain in my left knee (pain on inner kneecap). I limped home and rested it up for a few days but missed the Sportive altogether.
Since then It just won’t heal. I started by trying to self-diagnose and treat. Foam roller, stability cushion, icepacks, Ibuprofen etc. No joy, so visits to 2 separate physios (one through work, the other as part of a Retul assessment/fit) who have both said there’s nothing majorly wrong with my knee other than overuse. They both gave me stretching (hamstrings, quads) and strengthening exercises (glutes, hips). One diagnosed a fallen arch on my left foot, the other (more specialised in cycling physio) said I have limited mobility in my left ankle which causes my knee to turn in. Both noted that my right leg is much stronger than the left. I have since purchased custom orthotics and had a professional bike fit, which mainly led to the saddle being brought forward and raised by a not insignificant 30mm….. It no longer conforms to the height setting using the heel method (its much higher).
I’ve religiously done my exercises twice daily, cut back on rides (5 mile commute once/twice weekly, occasional 20 mile ride at high cadence and no hills). However over 4 months it hasn’t improved at all. My knee continually clicks, my shin makes cracking noises. If I sit for any length of time (my job requires it) it aches. If I do a lot of walking it seems to improve, but returning to work/sitting and the ache returns.
I suppose I’m trying to understand whether I have to accept that this might be permanent (neither physio thought so), or I am being impatient, or even whether someone can share tips on how they recovered from a similar problem? Should I abstain from all cycling for a prolonged period? I’m 44, btw, and otherwise quite fit.
Anyone care to share their own experiences? Thanks all!