Two out-of-the-box options, which do not require customization:
1) Use separate Locations with Stockkeeping Units and Multiple Production Orders:
Output your WIP Item from a Production Order at Location 1. Transfer the WIP Item to Location 2. Consume the WIP Item to produce either a secondary WIP Item or the Finished Good. Transfer the WIP/FG back to Location 1. The Planning Worksheet can suggest all required Production Orders and Transfer Orders, as well as component purchases.
2) Sticking with the separate Locations but using a single Production Order:
I would recommend using Bin Mandatory at each Location and setting the Components at Location on the Work Center Cards. This way the single Production Order creates component demand at the different Locations. Instead of a Pick being generated from Location 1 for production at Location 2, the Pick will be created for Location 2. A transfer order would be utilized to move the product from L1 to L2 ahead of time, so it is ready for Production based on the Route. Again, the Planning Worksheet can suggest with the Prod. Order Creation and the component purchases and transfers.
If you stick with your current setup, you should increase your "Move Time" on the Route to account for the long transportation time required during the Pick.
I hope this helps. I would suggest you schedule time with your partner to discuss this in more detail and see it in action.
Best Regards,
Ben Baxter
Accent Software Inc