Longer or shorter cranks, at least at the increments you're talking about, won't do much to ease pain, not by themselves. Look at your cadence, saddle height and set back, cleat position, pedaling style.
Cadence - I'm sometimes a pusher, rolling up big climbs at 40-50 rpm for 1-1.5 hours at a time. Cadence alone doesn't ruin knees. However, higher revs with lower torque reduces stress on the knee. Lower rpms will accentuate any position or pedaling problems. The problems at "lower" cadences suggest that something needs correcting (which you agree with, since you posted a question on a possible fix).
Saddle height - as you pointed out, if you have pain at the back of your kneecap, raising your saddle can help. I've done this to alleviate overuse symptoms, but ultimately the saddle should come back down. Too low and the kneecap starts to get sore again.
Cleat position - too far forward or back and you'll feel some pain. I find that having the cleat closer to the toes makes my Achilles get sore, too far back and I just lose speed. Angle is critical, meaning which way your foot points. For me angle is the most important thing, and I adjust my cleat so it's in the center of its range of movement so I have full movement in both directions (currently 2.25 degrees, since I have 4.5 degree float).
Pedaling style - a choppy stroke won't help your knees. You can reduce peak torque by putting out more power on other parts of the pedal stroke - pull up hard (hamstrings, esp if you keep your foot a bit level), pull over the top (quads).
For the record, I ride 4-6 hours a week right now, at a middling pace. I'm not very good aerobically but have decent peak power. I race during the warmer months, and I train maybe 4-8 hours a week during the summer. I do some "training camps" where I cover 25-30+ hours a week. I have a 29" inseam, ride a 52 cm Cdale or size S Giant, and ride 175 or 170 cranks, depending on my next goal.
Right now I just switched over to 175s, in preparation for March/April.
cdr