1) Could you specify those five directories you've uploaded on server?
2) Check, whether there are the patch files:
- patch_4_1_12.diff
- patch_4_1_12.sql
if so, try to apply them as the regular X-Cart patches:
-
http://help.x-cart.com/index.php?title=X-Cart:Applying_Patches#Applying_File_Patches
-
http://help.x-cart.com/index.php?title=X-Cart:Applying_Patches#Applying_SQL_Patches
Note: the other X-Payments Connector files must be on the serve before applying the patches.