@ShawnSlavin I'd add the following advice for setting up MRP:
All items must be assigned a primary vendor - if the part is made by your customer, then they are the primary vendor.
All items need a standard lead time - best calculated from a quick crystal report of last purchase order date vs. last receipt date.
Clean up all stragglers in SO, PO and WO - if the order's no longer active, close/delete it.
You can use the reorder point (qty tab, then the icon on the right) for items to create the 45 day buffer needed, and then you don't need to think about again.
Do they have multiple warehouses? Make sure you have them setup correctly in MRP.
For work order - run the purge to history option off the main menu (first check the WO setup options for the number of days to retain closed WOs). This will move the old closed WO to WO History and speed up MRP generation.
You didn't mention Bill of Materials - are they using that module too?