The difference is that all though both assemblies are composed of parts that are required in order to run a vehicle. The cylinder heads themselves are the main difference. The long block assembly is the completed version of the short block, and with all the needed internal parts. With a short block, you will need to acquire additional parts and they also have a longer installation time. Basically the short block is the more expensive when in comparison of the two. Long block assemblies will also help you maximize performance output. The fact that it is already in a completed state, also allows the components included in the sub-assembly to wear out more evenly, minimizing future replacement costs.
First and foremost it is the cost. The additional external parts associated with a long block are less expensive. When compared to the internal short block components. Labor charges for instillation are also less expensive, because this sub-assembly requires less installation time.
You have to do your research though, not all long blocks work well with particular vehicle’s make and models. Although a long block is already a completed assembly, you will need to confirm that the transmission and control modules are compatible with the long block before purchase. Also, you will need to confirm the fit with the shift linkages, axles, sensors, wiring harnesses, and mounts before deciding on replacing your engine with a new long block assembly.