Very nice interface! It sounds like you might want two separate steps and two separate CGIs (or one CGI with a "step" flag). Here's one idea:
1. Pass the configuration info from the form, initiate the measurement, and return a confirmation page to the user. Embed something in the result page (a hiddden variable on a second form, perhaps?) that will identify the measurement that was requested upon a subsequent CGI call.
2. Either have the second form/CGI automatically submit itself after time T, or else allow the user to submit it. Use the hidden variable to identify which results set is being requested. If the measurement is finished, return the results; otherwise, return another confirmation page with a new time estimate.
Best of luck,
Jo
hn