It sounds like a lot of the problems you are having will be improved by getting a road bike with the proper fit. If you are already doing 40 mile rides I agree that you would likely outgrow a flat bar bike pretty quickly. The hoods are the "neutral" position, this is where most people spend most of their time riding. The drops are nice for descents and the flat top is nice for climbing, but all of the positions can be used at any time to change things up and make it more comfy for long rides. I pretty much only use my drops for descents. Womens' specific bikes are generally designed for a woman's shorter torso, however many women fit better on non-womens' specific bikes. Two of my girlfriends had the same problem I did with "men's" bikes, in that the brakes were hard to reach. Often times this can be adjusted with shims. I have a Trek 1500 WSD and I have no problem reaching the brakes (I also have very, very small hands). The knee stuff is likely due to saddle position, your saddle may be too far back and/or too low. Your LBS should be able to fix that one easily, or keep tweaking yourself until you get it just right. I also had a lot of girly bit mashing going on which was fixed by both better shorts and a better saddle. High end shorts have a more thoughtfully designed chamois that narrow between your legs and provide support in the right places (as opposed to a lot of low end shorts which just put one large piece of round foam in there, which works ok for some people). I am still trying out my new saddle to see what I think, a Terry Butterfly Chromoly Gel, and so far so good. The cut out and the flat shape help a lot. Good luck in your bike search. Ride lots of them and keep going back to ride the ones you like until you have it narrowed down.