I would like to point to MO's article a few weeks back about buying a bike. Have you established what type of riding you'll be doing? Clearly, a 999 is not a realistic option for the criteria you briefly listed, but you can persue sport-touring, standard, cruiser, etc.
Many bikes can have their bars swapped for different rakes, heights, widths, etc, just as you can with bicycles. Even if you're interested in a sport bike, you can often find more comfortable clip-on's (Helibars) to bring the grips up and farther back. Similarly, Sargent Cycle and Corbin both offer an impressive selection of more comfy seats for many popular models.
Also, just yesterday I was discussing with a friend how some body types just match a certain bike better than others. My friend, for example, finds my Mille very comfortable for a sport bike, while I experienced lower back pain for a week and a half until my body adjusted to the sport bike I just transitioned from.
Good luck.