I would actually start by letting your knee heal up a little bit. Use a bit of ice to tamp down the inflammation, but sparingly -- too much and you'll injure the tissues in your knees. 15 minutes of ice, at least 45 minutes without. Try not to do the kinds of rides that aggravate your knees, or take a few days off.

Then, start figuring the issue out. My initial thoughts, as with some others, is bike fit. You can try raising the saddle, but may be better off ponying up for a real fit with someone who knows what they're doing, and perhaps make a few tweaks. I'd also think that especially if you plan to put a bike together yourself, getting the right fit will head off any issues.

I'm not entirely convinced that an ultra-light bike will help much with the knee issues. What a different bike will offer you is just a different ride experience on those 40+ mile rides, a different rider position, and an opportunity to use lower gearing if you choose. Most of the benefits would likely be in your lower back and hands; a more flat-back position takes some weight off the saddle, and drop bars gives you more possible hand positions.

I don't think you'll notice a big difference between steel and aluminum, especially with newer AL frames. My understanding is that Ti tends to have the same road feel as steel, but with a little less weight, more corrosion resistance and much much more expensive. CF will probably produce the biggest difference in ride feel, but unfortunately you'd have to test ride something to see if that's the case for your level of sensitivity. Plus it's spendy.