Some good advice. What I would do, and some of this will repeat the prior advice:
- Raise seat to the correct height. Place your heels on the pedals, and pedal backwards, the seat should be as high as it can be, your leg fully straight and just reaching the pedal at the bottom of the stroke, without your hips having to rock from side to side to reach the pedal. When the balls of your feet are on the pedals, your knees will be slightly bent and your ankle slightly flexed. This is very important. A low seat is very bad for knees. Imagine getting down in a crouch with your knees deeply bent, and trying to waddle for a mile, your knees would be in agony. Riding with a low seat is equally bad.
- Do not pedal with any significant force, at a cadence any lower than 80 rpm. It will feel like you are spinning your legs too fast. Get used to it. Pedaling with high force at a low rpm, "mashing", is another prime cause of knee pain. Pushing too much force through your knees hurts them, so instead push half the force, twice as often. You'd hurt yourself lifting 50 lb, but you could lift 25 lb twice no problem.
- When climbing, try to stay seated and spinning a low gear at 80 rpm or more. Standing pedaling is hard on the knees too. Same principle as above. You stand in order to push more force, but that is what you don't want to do.
That should help a lot. But I think you should go further and use clipless pedals.
- With platform pedals, you can only push down, with your quads and that works your knees hard.
- With clipless pedals, you can pull back, using the hamstrings. You can pull up, with your hip flexors. You can push forward. Those are not as strong as pushing down, until you build up those muscles. But it takes some pressure off the quads and knees, and eventually you will "pedal in circles" and be much more powerful than when you only stomped down.
- Most types of clipless pedals have float, which protects your knees. For commuting, SPD work well. There are pedals with SPD on one side and platforms on the other.
Thanks for that advice, I think you've summed it up quite nicely, everything makes a lot of sense.
What can be done to improve the comfort on the saddle? I'm using the original one (Bontrager) which is small, but I've been wondering if it's a good idea to put a foam cushion on top of it so I have less issue with it.