You can use the Admin API to set a customer's password. So in your case you would need to be able to decrypt your existing passwords and then set them so that they were encrypted for KonaKart:
From the Admin API javadoc:
setCustomerPassword
void setCustomerPassword(java.lang.String sessionId,
int custId,
java.lang.String newPassword)
throws KKAdminException
Set a customer's password. The new password is set for the customer. No email notification is sent.
Parameters:
sessionId - The session Id of the logged in user
custId - Customer Id
newPassword - New password (as entered by the user)
Throws:
KKAdminException
From the Admin API javadoc:
setCustomerPassword
void setCustomerPassword(java.lang.String sessionId,
int custId,
java.lang.String newPassword)
throws KKAdminException
Set a customer's password. The new password is set for the customer. No email notification is sent.
Parameters:
sessionId - The session Id of the logged in user
custId - Customer Id
newPassword - New password (as entered by the user)
Throws:
KKAdminException