Generally speaking, short stroke engines are revers. Long strokers offer more torque.
For example, air-cooled boxer-style aircraft engines, be they 4, 6, or 8 cylinders are l-o-n-g stroke. The popular Continental O-200 has a take-off limit of 2750 rpm for five minutes. The classic P-51's Rolls Royce Merlin, a liquid-cooled V-12, had a 2600 rev limit at 12250 feet ASL.
Increasing an engine's stroke is usually accomplished by using a different crankshaft; often referred to as a stroker crank. Attempting to bolt in longer -this is a relative term as to rod length discussion- custom con rods could be asking for trouble with valve interference. Either way, results would most likely be minimal. The BMW R65 has been the victim of hot rod techniques many times in the past. I have yet to hear of anyone's quantified success.
Swapping the final drive is probably the best option. I would think the higher gears would provide a potentially higher cruise speed only if the bike's load out weight was carefully managed. Load the tank bag with a map, clean t-shirt, shorts and socks, you're good to go.
Lots of R100s out there for sale. [smiley=bmw_smiley.gif]
Monte