AFAIK, the uStore WS API is not designed to programatically add orders. - You can only get product properties and customization dial values - not set them. Like you found, there are no methods for setting delivery.
The way I have seen uStore integrated into other systems, is to create your store as a "uStore Connect" store type, and to load the uStore URL into an iframe or pop-up windows in the custom application.
There is a uStore connect sample provided with the uStore API SDK.
Also, remember, that to use the uStore APIs legally, requires payment of an an extra licensing fee to XMPie that may or may not have been purchased for your system.