I know exactly what you're talking about. Unfortunately, most road bikes are all wrong for a dirt guy. I've just become used to it a bit. I actually find that the width of the bike at the tank affects me the most now.The best thing I do is stop frequently to stretch my poor aching knees and back out.
You could look at it from the other direction and modify the seat. Maybe out a little more material on top and in front to give a little more legroom and make it a little narrower? A little here can go a long way, and it's usually not very expensive to get an upholstery shop to modify the seat (even cheaper if you're handy with a staplegun and do it yourself). I know the 1250 has an adjustable seat you could raise, not sure about the older ones though.
There probably are some aftermarket solutions out there for pegs, some people put pegs on engine guards to stretch out a bit as well. Do a search, and good luck!