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"Runner's knee" is a common complaint among runners. How did you overcome this obstacle?

I got to week 8 day 1 this week with more or less no problems. This is a massive achievement for me because previously when I have tried to run, I have suffered a lot from muscular aches and pains, in particular around my neck, shoulders. It is like my cardio-vascular fitness outpaces what my muscles and joints are able to do and I end up very sore! This programme has been fantastic for me because the pace has made it possible for me to really concentrate on my form: my posture, my footfall etc. and build up my fitness and strength while running really slowly. However once the runs got to 25 minutes+, I began feeling the ache around my knee for about 24 hours after my run. I have an old knee injury, not running-related which I had intensive physio for about 10 years ago. The last 28 minute run really made the next day very uncomfortable for me. So as I can't really justify being out of action every second day I've gone back to the beginning of week 6 to see if I can build up my muscular strength more gradually. And I know I have to do some strength and flexibility training on my non-running days, so I've started doing a YouTube running video. Secretly I'm quite pleased to be back doing the interval runs as I miss being told what to do every few minutes! However, I feel like the post-run aches in my knee and my hips have been around for ever, no matter what kind of strength training I have done. I'd be so disappointed if I can't make it to a 30 minute run without suffering the next day. Any tips or experience anyone could share? And yes, I do stretch after each run!