Phil,
have a look at this
http://pixinsight.com/forum/index.php?topic=1563.0 becasue it is one thing that i will be looking at when i go to Qld Astrofest as i was going to do the same thing (but no where near as good as yours - was going to use a 135mm lens).
this method within pixinsight allows you to obtain a seamless intregrated result.