since you are using one package for entire order, the package quantity should be set to 1:
change:
$Shipping_PackageArray[$Shipping_PackageIndex]["Quantity"] = "".WA_eCart_FormatNumber($eCart1->DisplayInfo('Quantity'), true, 1) ."";
to:
$Shipping_PackageArray[$Shipping_PackageIndex]["Quantity"] = "1";