Build A = Expensive Build
Build B = Cheaper Builder
The difference is not much, Build A motherboard has 10 6GB/s Sata ports where as Build B has only 6. Otherboard than that is the processor support for each. Build A has a newer processor - the Haswell line. Performance difference is very little - not enough for the money. However I believe Intel will be using the Build A socket in newer processors, so if you think you are going to upgrade in the future, go for Build A.
For more performance I would suggest an SSD to install your OS on to.