What are the manufacturing difficulties for a large Li-Ion battery pack?
Like horta said, battery grade lithium (~$5.00 USD per pound) is quite expensive compared to steel (depends, it can be less than $1 USD per pound) or aluminum (also usually less than $1 USD per pound) used in an engine block. 

Lithium likes to react with the atmosphere, forming lithia/lithium oxide. Refined lithium or just lithium in general will likely require special handling, also increasing costs. There are quite a few regulations regarding the shipment of lithium.

Large Li-ion batteries or cells, especially in cars, can pose a safety risk when they are punctured or exposed to atmospheric oxygen. Just google, "exploding li-ion battery". Having smaller/individual cells like 18650 batteries could help minimize the amount of lithium that is exposed when the is battery damaged. However, having a greater number of smaller cells can increase the cost of manufacturing as they could easily be more sophisticated (cooling, wiring, assembly of cells etc...)

In conclusion:

Main costs of large Li-ion batteries:


Cost of transport (special requirements)
Cost of battery grade lithium
Cost for manufacturing large numbers of small cells
Cost for assembling small cells into a large battery