Hi Tim,
Disclaimer: While I am a junior doctor, I have neither examined your knee nor do I know your previous health status, so cannot make a certain diagnosis or perfectly adequate recommendations. I cannot take responsibility if you follow my advice and you try it at your own risk, everything I write below is what I would possibly recommend after careful examination and interviewing and might possibly help, also trying to explain a bit why I would do it this way. Other doctors might recommend different things and be right in doing so, as there are always different ways of approaching medical problems. This is not meant to replace seeing a professional in person who can examine and interview you and cannot replace physical therapy, just some thoughts on what I would possibly recommend. I will not take any liability if it doesn’t help or get worse.
I saw you found Jonathan’s thread for knee problems, which is great, a good idea is to try as many of the suggested solutions (especially regarding exercises and PT) recommended there one by one or maybe even several at a time until you find something that helps and then stick to that. It may take several weeks for the pain to go away even once you’re on the right track, so don’t give up too quickly.
Icing is good and does no harm (unless too cold and you get frostbite on your skin) and can also be done via ice cold showering of the legs/knees after training.
Ibuprofen will only relieve pain short term (and negatively impact any endurance progress if taken regularly) but will not fix the underlying problem if it is biomechanical of origin (which it often is in chondromalacia patellae). What you can try is taking one course of Ibuprofen up to 800mg and 3x a day for 7 days (depends on your bodyweight and other health status, unless you’re <60kg or have liver, kidney or stomach issues, 3x800mg taken with meals should be fine. If you have too much acidity / reflux / have had a stomach ulcer, shorten the course to 5 days and/or use Pantoprazol 40mg once a day in the evening during the course and for 2 days after the course of Ibu has finished). This will help reduce an acute flare / active inflammation to a minimum. This should not be done too regularly (aim is not to do it more than once at all) and is only intended to get rid of active inflammation so you can start your physical therapy. Also, complete abstinence from anything that elicits the pain during this course is necessary, otherwise you’re setting a new inflammatory stimulus and counteracting the medication. Taking Ibuprofen here and there will not help as long as the underlying issue is not resolved, as said.
Next up, I would check out your cadence: too low → not good for the knees, anything above 85 would be good, don’t go near anything below 70.
Underlying principle: too much tension in the quads transfers to the patellar ligament and pulls your kneecap onto the femur.
This extends to:
very high power intervals;
individual leg training;
anything else that puts a lot of strain on your patellar ligament repetitively.
Note: strength training (including squats) should be fine, as you’re not in for 85+ reps a minute but likely 25 in total. Maybe don’t squat too deep (i.e. below 90 degrees bend in the knees) and maybe not in the acute phase or while you’re on the ibuprofen course.
Next, cleat position and knee movement. While the bike fit may have been good in the past, something isn’t working with your biomechanics now if you’re getting pain from cycling.
Check out these:
knees tracking straight;
angle of your knee joint during max force production (i.e. at 3 o’clock in the downstroke) should not be too small/narrow (meaning get closer to 90 degrees bend in the knees rather than 30 degrees) → might have to move your cleats backwards on the shoes to move your feet forward;
saddle position might be too low or too high (again, influences knee joint angle);
cleat rotation (inward / outward rotation could cause this problem);
lateral offset of the pedals helps for some people, i.e. insert spacers that set your pedal bodies further away from the bottom bracket (this might also be asymmetrically wide left and right, meaning more spacers left than right or vice versa);
If none of this works, give yourself a timeframe to keep trying, for example 6 months. If you’re not back to normal then, see a specialist, try getting an x-ray of your kneecap to see if it’s weirdly shaped (that causes issues often) and/or an MRI to see if something else is wrong. In such cases (long-term problem keeping you from training or weird kneecap alignment), the last resort might be a cortisol shot into the knee joint, which sometimes works wonders (it works like the ibuprofen course, but on [literally] steroids), but should not be used too lightheartedly and might have to be done several times to take effect plus you need to keep doing your PT. This has to be done by a professional who has done this many times before.
Will say this: runner’s knee is a vague description that means many different diagnoses to different people. My understanding of runner’s knee is a tightness of the tensor fasciae latae and fascia lata (fascia on the outer side of your thigh) causing a stabbing pain on the outside of the knee due to inflammation of a bursa (a little “cushion” filled with gel to buffer any lateral friction there). Very different story. Short summary solution for this: Blackroll the side of your thigh, strengthen your lateral hip muscles / abductors with e.g. side planks and banded side steps (stretch band around the knees above the kneecap and walk sideways). It will go away if you do this and stay away as long as your lateral hip stabilizers are strong. Cycling doesn’t make them, running doesn’t make them, you need to train them. Those and your core are the two essential things you need to train outside of your endurance workouts to keep you healthy and training (especially if you do any running).
Bonus insights while I’m at it, that may help you and others:
Injuries and strain occur all the time. If you stop every time something hurts a little, you’ll die from a heart attack due to inactive lifestyle. If you never stop even if something hurts badly, you’ll need new joints due to osteoarthritis (not what you want, especially not knees). Knees are a very whiny and sometimes overly sensitive body part, they hurt all the time for sometimes no reason, but pay attention to them and if it’s longer than a few weeks or reproducible in certain circumstances then adress it quickly. I’m not saying train through all pain, but you’ll (have to) learn to differentiate between pain that you have to take serious and ‘discomfort’ that you can ignore.
Don’t skip PT exercises. Don’t skip strength training. Eat your 2 pieces of fruit and 3 pieces of vegetables EVERY SINGLE DAY. Pay attention to your form. Bike fitting is not a one-time set it and forget it.
Ibuprofen doesn’t fix any underlying problems, ever.
Find a good physical therapy or read up yourself and do your PT. Regularly. Forever. It will keep your body healthy enough for training, which will keep your cardiovascular system healthy enough not too die at 65 (and exercise also prevents cancer).
If you can’t run because you’re injured, try cycling (depending on the injury location). If you can’t cycle, swim. If you can’t swim, do strength training and go hiking/regular walks. If you can’t lightly strength train with bodyweight and walk properly, go see a specialist and get this fixed asap, something is seriously wrong. 
Added for anyone with this problem (chondromalacia patellae) who is a runner: increase your cadence, which will automatically make your steps smaller and your feet will land closer to your centre of gravity, which is a lot better for your knees. Science says which part of the foot you land with doesn’t matter for injury, but where your feet land in relation to your centre of mass does. Big steps → bad, small steps close to or right under centre of mass → good. Anything above a cadence of 85 works for ultra-endurance runners long-term (most are above 90), there are next to no long term successful long distance runners running anything below this cadence, which possibly tells you something about the longevity of those other runners’ knees who didn’t perform for decades. Or at least it’s a starting point and has no drawbacks. 
Not being able to train as you want can be frustrating. Accept, that this will occur regularly and you will have to include prehab and rehab into your training plans. Depending on your luck in the genetic lottery it might be all the time or it might be once every couple of years. You can’t change the fact that this occurs, but you can change how you view this fact of life and what you do about it. Make a habit of staying positive and keep a mindset of “what can I learn from this, what is my body telling me”. It helps with the mental side of things. It’s a challenge you are ready to face and will solve, not the end of the world, even if it may take months or years.
Good luck!
Stefan
