Yes this is possible. With our new shipping system that we setup last month you can setup shipping rules for different locations.
Go to Seller Admin>Edit E-junkie Cart Shipping Settings. First, remove the 1.99 shipping from the handling fee area and then click the Next button. On the next page you can create shipping rules for your products. A more detailed a rule will override a general rule. First lets create the general rule. Use the Shipping Rate Calculator dropdown and select Flat. Type in the 3.99 for the amount. if this is the rate no matter what is ordered leave the rest of the information as it is, the country dropdown should be All Countries. Then click Submit. Now start a new rule, select Flat again and set the amount to 1.99 and select Canada as the country and click Submit, repeat for the US.