my advice for people with knee problems is to strengthen your quads. A great exercise, even without weights, is leg extensions. you can even do these at your desk at work. Extend one leg by slowly raising your foot all the way until your leg is straight and hold for 3-5 seconds while flexing/tightening your quad muscles as hard as you can...do 10 reps. Then do the same on your other leg. This helps not only strengthen your quads but stretches your hams. Do a couple sets of these at least every other day and I guarantee your knee problem will get better. It's also good for people like me with lower back problems.
My '93 civic was a manual, and i had to adjust the seat much closer to the front. I'm 5'8" too, but my legs are a bit short and my torso is a bit long proportionally, compared to most folks. Nothing unusual, but maybe that's why I never had knee problems; instead I had back problems/sciatica that made it very painful in my left leg all the way into my foot. Seriously, i was f*cked up and couldn't walk for certain periods. I had back surgery in '94 but it relapsed a couple times since then. The closer I sat to the front in my manual civic, the less strain I put on my back, so I'd drive around like an old granny and it probably looked funny but it was more comfortable when working the clutch.
One reason I'm loving my '06 civic so much is i can sit much further back now. The seats seem to provide more lumbar support, too. Anyway, i didn't mean to hijack your thread with my back problems. Try the leg extensions and that should make your knee stop aching.