On your annotations, let us address them one at a time:
Need to address Row Alignment:
You have missed out a blank array element at the last:
Lines 144-146 in sales/includes/ui/sales_order_ui.inc
$th = array(_("Item Code"), _("Item Description"), _("Quantity"),
_("Delivered"),
_("Unit"), $order->tax_included ? _("Price after Tax") : _("Price before Tax"), _("Discount %"), _("Total"), "");
For you should be:
$th = array(_("Confirmation"), _("Source"), _("Avg Rate"),
_("Stay"),
_("Gross"), $order->tax_included ? _("Our Charge") : _("Price before Tax"), _("GDS"), _("Total"),"");
Check if you also need to increase the col span for the other rows at line 225 (of the original file):
$colspan = 6;
to be
$colspan = 7;