I would start with ADempiere as a model. It is an open source ERP that has good ties to accounting and storage. You can see how they implemented material receipts, inventory moves, physical inventories, cycle counts, and shipping...
You are correct in that the domain is deep and wide with many ties to other areas. There are ties to lot number management, fifo, lifo, etc...
Here is a review I wrote about ADempiere. http://www.chuckboecking.com/blog/bid/196464/ADempiere-Review-Open-Source-ERP. I believe this document will help you think through the domain. It will also help you understand how to use ADempiere if you do want to use it as a model.
Good luck, and I hope this helps!!
Chuck Boecking www.chuckboecking.com