Have you been to a doc to try to find the cause of your cranky knees? I assume that since you were a runner (first) and stopped running that you have already been down that path, but figured it was worth asking.

I had a knee problem a number of years ago that was tagged as an overuse injury - and who knows whether the cause was cycling or something else entirely... I assume that it was cycling because the problem cropped up after I did a century in lousy weather (cold and rainy) and followed that immediately by a week of hilly and cold riding in Vermont. (OK, don't say it, I know I'm a bit crazy!) Luckily this happened at the end of the riding season. The problem disappeared when I stopped cycling for a few weeks, but as soon as I got back on the bike it reappeared. Tthe orthopedic doc put me on anti-inflammatories and referred me to a physical therapist who gave me exercises and who I worked with for probably 4 to 6 weeks. Whatever we did - specific exercises or other treatments - solved the problem for me.
Although working through pain sometimes works, I'd rather see if the cause of the problem can be found. It makes me a bit nervous because I worry that I could be doing further damage.

Does riding the trainer hurt too? I don't know your riding style - are you spinning with low gears, or are you pushing higher gears. If you're not already using low gears, it might be worth a try to switch your riding style. My inclination is to give your knees a rest. If it's 2 weeks until your century you're probably already in decent shape and ready for the ride. If you're anything like me, you don't want to stop exercising - which is why I suggested using lower gears - and maybe doing that on the trainer would be a good idea. I guess my vote given the three options you listed are either for 1 or 2.

Keep us posted on what you decide to do - and on your century too!

--- Denise