Company File Setup
Make sure that the checkbox "Inventory and purchase orders are active" is checked in preferences under the "Items & Inventory" section.
1) How do I connect QuickBooks with Finale when both already contain entries for the same products, customers, etc.?
Make sure that the field documented as connecting the two entities (e.g. the Name field and the Display name as field for customers) are exactly the same in the two systems before syncing the first time.
2) I am getting an Intuit 401 error when attempting to to QB
That API:HTTP Error 401 means that Finale Inventory cannot access your QB file. The cure for this is to remove the integration, then Add it back. This process will require you to re-authorize the connection between Finale Inventory and your QB Company file, which will fix the problem.
Go to Add-ons & Integrations, then go to the Actions menu and Uninstall integration, choose QB. Then, Log off and close the browser. Then, Log back in, Go to Add-ons & Integrations, and Actions, Add the QB Integration back, then Click on the Connect to QB button, and it should ask you to re-authorize.