Hi Andrew,
As others have said, this sounds like interesting work.
From what I have understood you are wanting either the browser or the Moodle software on the web server to call a web service on the computer of the person acessing Moodle to check if they have put a file in the right place and/ or with the right permissions?? Or is the web service on the server and the person has to place a file in the correct place on the server?
The reason I ask is for me / us to get more of a grasp of what you are trying to do and because if the web service is on a web server then there wouldn't be any network access issues but outside an internal LAN then I think you are going to have access problems trying to call a web service on the client computer.
IF you are trying to check for a file on the server why not use php's file functions to do this rather than calling a web service?
I think in an answer to your question about when to call the web service you probably need to put this in the code to evaluate a student response, browse through the code of outher question types to see how this works. But you should be aware that this code to evaluate student responses will also be used when a question is being regraded, so you need to work out how to stop the web service being called in this case.
If you grade a question wrong in ínteractive response' mode then the student will have the chance to do the question again. This might give you the chance to give the kind of feedback you want to to students. You can adjust the feedback given to the student by changing the 'feedback' property of the answer object you return from the response evaluation.
Jamie