This is the reply i got from Telerik
"The problem comes from the fact that in Sitefinity 7.0 was made significant code refactoring making not possible your case.
I have consulted also with our developers from Sitefinity eCommerce who explained that an internal method in OrdersManager (UpdateProductInformationInCartDetails) re-calculates all cart details and total price for the shopping cart. It is called in ShoppingCart widget, ShoppingCartSummary and CheckoutWorker on the first step of the checkout process. In other words the three widgets should be re-written to skip this call and call a custom one.
I am sorry for the inconvenience caused."
I ended up overriding the InitializeControls method in the ShoppingCart and Checkout wedgets. In those methods i called a helper method to extract any custom prices from the deltaprice on all items in the cart then called base.InitializeControls. Then I called a second helper method to reapply all the custom pricing and recalculate the cart total. Everything seems to work great. I also ended up having to modify the layout for the orders list as it was pulling the product price from the eCommerce product instead of the order.