Using the Periodic Inventory method - the end of the period inventory count is 539,930. To adjust the entry do I
Credit Inventory 539,930
Debit Income Summary 539,930?

No, you have 539,930 LEFT.

You need to subtract that amount from what your records say you have on stock.

Then you credit that difference to inventory and debit it to COGS.

Thanks so much. :)