Hi Jenz,
You have two common questions:
1) How to programmatically load the InfoPath form? Chapter 9 in our book discusses this - there is a ListItems object and you can use HTTP, DAV protocol or the ShP WebService to open them. I prefer just HTTP. You can even just add a link to the xml form stored on the site that will open the form through your Java portal. SharePoint also has an open XML document method that you can call from java to open the form through the InLaunch.dll via the registry key for the XML document object in your registry. Sorry for not being more specific but it's late here and I want to go to bed ... :)
2) How to store SubmittedBy user info with the form?
Use ActiveDirectory to get the name and then add it to your form and promote it as a property in your SharePoint library. Or, get the ModifiedBy attribute on the form that SharePoint stores.
Good luck!
Patrick Halstead
Project Manager at Qdabra