no, stroke is defently only determind by the crank shaft, no the rod legth. if you had a cylinder 1 foot tall with a 200mm diameter, and was 100*1/pimm from top of the cycle, to the bottom of the cycle, then the displacement of the cylinder would be pi*r^2*throw or pi*100^2*100*1/pi. pi's dorop out and your left with 100x100x100 =1,000,000 mm^3 or 1,000cc's. Notice there is zero refrence to the rod legth. The rod could be and inch tall or just under a foot. Only diffrence would be compression ratio and combustion chamber size.
As for your question, yes b-series crankshafts are diffrent from model to model.
For example, the only real diffrence between the ITR and CTR minus compression and some other stuff like the cams is the crank. you put a ITR crank in a CTR, then basicly get a ITR engine with a b16b stamp on it. You will have a 1.8 liter CTR. Same thing with an ITR engine. You put the CTR crank in there, then you get a 1.6 liter ITR engine.
In your case, just get a GSR crank.