The checkout forms that eCart 5 creates are going to show the full name of the country for the label and the abbreviation for the value. So a user who is from The United Kingdom would Select United Kingdom from the menu and the value that is held and passed around will be the abbreviation for this country 'GB'.
So it seems this would satisfy all of the needs that you have for the country abbreviation from the checkout page onward. The only thing missing would be to set the country select list to the value held in the record for the user. The user would need to have the country abbreviation stored in their profile.
To do this you will need have a way of identifying the user. Most of the time you would have their id held in a session variable. Then on any page that you would like to reference any details for that user would need to add in a recordset that is filtered by the identifier for the user. So if your logged in user had a session variable called id that was set to a proper value you could filter a recordset to get back all of the info for this user by choosing the filtering options then specifying your id session variable.
Once you have the recordset on the checkout page you can use the dynamic options to select the value that is equal to that column from your recordset. This should prepopulate the country select list on the checkout page.