I'd recommend you to go for a clean Kabuli assembly/engine. Rebuilds rarely turn out to be good. All mechanics claim that the engine would run like zero meter and once the engine is rebuilt and you see issues with it, you'd hear them say 'sir factory se to nahe ban ke aya na itna hota he hai rebuilt engine main'. Engines, when they leave the factory, they are assembled with a lot of precision, torqued to spec and many other parameters are controlled. The local mechanics do not follow any such parameters.
You need a good mechanic who can tell the state of the engine by looking at the internals of a Kabuli engine. There are different signs on an engine that help you determine how much an engine has been run and the health of the engine as well.
How is your current engine behaving? What clues has it given that have made you want to replace/rebuild it?