Java Programming

I have a client who needs data pushed from one system to another but the only way to access the destination is via a Java applet running in a web window hosted internally. The source data is provided as a CSV. I have created many macros with Macro Express Pro to automate these batches but it’s method is to blindly fire mouse clicks and type in a way to emulate a user. Due to timing issues and environmental variations it’s very difficult to write code that will work reliably in large batches or aren't excruciatingly slow.
I write a bit in VB.NET and for other clients have automated things like this using HTTP request/response, browser controls, or other automation APIs to do similar things and would really like to do the same for this client but so far the applet’s controls appear invisible to the browser and there is no HTTP traffic so I’m guessing it’s using RPC.
My first question is if an applet can be run outside the web browser somehow. If it can be I might be able to set up a more stable environment. Also it might expose the controls as Windows controls that would be visible to Macro Express.
Next question is if there’s any way I could write a program in VB or other language that could automate the form entry. Is there a generic API or would the developer of the applet have to have created an API?
Third question is if there is any simple and inexpensive testing software that might work for this. I know for other things there are load testing applications that run large batches of data matrix profiles for testing. Perhaps something like this could be used to automate? So far all I’ve found so far like AutoIT or MEP are blind and can only fire keyboard and mouse events at it.
Finally if anyone has any other suggestions of how I could automate this data entry more programmatically I’m all ears!