Hi, I don't if it could help, but I'll show you what I did:
in CheckoutConfirmationSubmitAction.java
in the method: public ActionForward execute(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response)
OrderProductIf[] articulosKK;
articulosKK = checkoutOrder.getOrderProducts();
for(int i=0; i<articulosKK.length; ++i){
articulosKK.setFinalPriceExTax( --my special price-- );
articulosKK.setPrice( --my special price-- );
articulosKK.setFinalPriceIncTax( --my special price-- );
}
I don't remember if I did something else, if I find something i'll put it here...
good luck