For the weight that is being passed you are only passing the weight for the first item in the cart. To update this on your confirm page update the code on line 49 to be like this:
$Shipping_PackageArray[$Shipping_PackageIndex]["PackageWeight"] = "".WA_eCart_FormatNumber($orphanoshouse->TotalColumn('TotalWeight'), true, 1) ."";
This is using the total of the totalweight column for the entire cart rather than just the first item.
As for the new shipping charges you will need to work out the criteria for applying the shipping charges a little more. For example if I have itemX that has a small weight in the cart and another item that has a larger weight in the cart what would you like to charge for the shipping?
I think you should base any new shipping rules on the total weight for the entire cart, if it is less than a certain amount then charge a flat rate. You can then edit the other shipping rule to account for this, you can add another condition to the trigger to check if the total weight of the cart is more than your low limit.
