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Knee pain when running and Quad pain when cycling

Question: Knee pain when running and Quad pain when cycling

I will try and keep this brief.

Background; I have a desk job so I am mostly sat down from 8am to 6pm. I started triathlon last year and have been doing a lot (short distance) running, swimming and cycling but at high pace.

Issues; end of last year I started feeling pain in my left hip flexor, and then in my left knee (outside tightness). I stopped running and continued cycling and swimming until i got a lot of pain on top of my left quad whenever i tried to put any sort of power down on the bike.

What I have done; stopped all activity in middle of January for 1 week and saw a physio (no diagnosis), stretched (hamstrings, quads and hip flexors) and foam rollered all of legs 3 times a day for 3 weeks, started resistance band training and general body weight excercises for 2 weeks and then incorporated glute strengthening excercises for a further 2 weeks.

Since then; I have done 3 very slow 3 mile jogs (lots of stretching before, during and after) with no pain. Last week I did a slow 9 mile bike ride with no pain. End of last week I did a very slow jog (no pain) and on the 2 mile gentle bike home (no power at all) i got another shooting pain in my quad. I have iced twice a day since and it still doesn't feel right and occasionally hurts when going up stairs.

I had at points felt almost knot points in my hip and quad which were painful to touch but I had worked these out and had none at the point I restarted running.

I have also noticed a have a lot of instestine noise although can't remember having any at christmas. Also my left leg appears to be smaller than my right, this could be due to years of playing high level badminton and lunging solely with the right leg!?!

I am concerned that I can spend another 11 weeks rehabilitating my leg again for it to go back to square one when I am exerting no power.

I am booked in at the doctors this saturday but fear he will try and tell me to rest. Do you have any suggestions / come across this before?

Any feedback would be much appreciated. It is very hard not being able to do what you love.