If you're looking for power, and not as much torque, a stroker probably isn't best. Some people wanting high RPM's actually de-stroke the motor (shorter stroke, same bore).
Basically, what you're looking at is the bore-to-stroke ratio. When they are equal, you have a "square" engine. When the stroke is longer than the bore diameter, the engine is "under-square." When the bore is larger than the stroke, the engine is "over-square." Most modern engines are square or over-square. The higher the RPM's you want to turn, the more over-square you want to be. The more low-end grunt you want, the closer you want to be to square.
Now, if you don't want to worry much about highway driving, an engine with a lot of low-end torque, combined with the gear ratios of that 700R4 and the 3.73 rear gears... well, that should perform nicely off the line. If you're worried about the 700R4 kicking down into 3rd, you should probably have it checked out - it should just kick down for no reason.
Also, there are aluminum guides that screw over the rod bolts for assembly, to protect the crank. No crank is really all that hard: with the beating it takes, a crank has to be soft - a hard crank would shatter. The bolt guides will protect the crank, and I don't think they cost much.
Joe