It doesn't sound like your frame is too big but it does sound like you are putting too much weight on your hands. Riding on the tops of the bars indicates (to me) that you were trying to get comfortable at the highest position the bar offered, at the time. Riding on the horizontal bar of the bar is not the best for the nerves in your hands. The handshake position on the hoods is the best from a comfort perspective and you should try to make that your best fit position. Riding the tops allows a more upright place to ride for a change of pace and the drops are nice in headwinds or when you need even more leverage for climbing or sprinting, than the hoods. If a cyclist always rides the tops, then the hoods are too low/far away and the drops are all but useless. For a touring bike, your position should not be confused with a racing position.
My bike is set up similar to
tpelle's with a 30 degree rise stem, 90mm long. This gets my bar several cm above the saddle and for me, with a short reach, it is really comfortable.
The cramping may have been related to insufficient water or riding past your fitness level. Soreness between the shoulders indicates too low/far of a bar position and/or exceeding your fitness level.
I can ride about 50 miles before any soreness becomes a factor and I believe my bike is fit well. I do know that my flexibility, weight, fitness and age make riding a long way a bit of a challenge with proper bike fit being important only to a point.
In short.....raise the bars and maybe make them a little closer (which they will naturally do, due to head tube angle) when you raise them. This will take weight off your hands, allow you to ride on the hoods, the flats will be a nice spot for a change of pace and the drops will become usefull for several minutes, without pain, when needed. Make your saddle level and move it back on the rails, if its not already. Lastly read
www.rivbike.com in their section on bike fit etc. if you are interested in comfort for long rides and not in looking like a racer.