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Go to a pysiotherapist (or two, or three, until you get some advice that works). Most likely it's a muscle imbalance issue. I really think this is the problem.
I had a knee problem with similar symptoms (didn't have the next-day problem that you have though) and my physio sorted it out in about 5 months, with a huge improvement in the first month or two (I couldn't walk initially). Muscle imbalances, endurance issues etc can be surprisingly debilitating if you haven't had a problem previously. It could just be one muscle that has deteriorated a lot, and when it runs out of steam (quickly) it can't get enough oxygen, and then you get pain and swelling in surrounding tissue because of an over-reaction by your CNS - and when that happens you might even find walking difficult. It doesn't mean anything is really wrong with your knee, it's just your CNS playing up. The cure (in my case) was to do a lot of endurance work.
If you really can't go to see a physio, do some squatting, lunges and deadlifts - up to 30 reps BW for endurance and then move onto heavier weights and lower reps. Work into the running VERY slowly with a 2.5+ minute warm up, and don't run faster than the minimum necessary to keep an adequate stride length, and warm down to a walking pace over 2.5 minutes as well. I was advised to use the cross trainer first, and that's what I did - this way I could also do cardio for longer. Gradually increase the time at the working pace by 30 seconds at a time, and once you get to 2.5 minutes at the working pace you can increase the speed by about 0.5Km/h every 30 seconds.
Knee problems are stressful, but with work they basically go away. I still get a bit of pain if I run for a long time, but I can run for 20+ minutes before this happens, and that's all I need right now so I'm concentrating on other things and not trying to improve it; at some point I'm going to go for a half marathon though.
EDIT: doctors generally know ****-all about this kind of thing, but there is real medical research behind it. Physiotherapists are really under valued by most people...make sure you get a good one though, as I think you are more likely to get a bad physio than a bad doctor.
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