So which POS system as advised under point 3 did you try? Retail business has also many skus and we use a separate POS for the inventory and sales and just import daily summaries.
So in your case all the inventory items and transactions would be setup and operated via the POS system. Then in Manager you do not enable the inventory module but you create a group called Inventory as a Asset and under that group you create any account that you would be able to summarize a financial total to that values the stock and also the sales because you would create a similar group and accounts under sales and under cost of sales. Then every day you would copy these summary totals in sales, cost of sales and value of inventory.
So the POS takes care of the Inventory (Asset), Sales (Income) from Inventory (COGS). Manager takes care of operating and administrative expenses, assets, loans, payroll (although if large number of employees would use separate payroll processor), equity, etc and generate whatever is needed for financial analysis and tax purposes.