Select a part of your mesh, i.e. saucer; then, depending on the location in max6 (I use 5), scroll down the modify panel until you see the attach button...click it, then select the part you want attached, such as the neck...it should now be one part. The attach button should be selected still, and you can keep clicking all the items until everything is attached together. Or, if it's available, there will be a button next to attach called attach list and a little button with a page icon...click that and you'll have a window open that lists every part you've made and you can select "all" then "select" and it'll be one mesh. That should take care of the problem. Also, when you boolean the mesh, you can attach the pieces, then in vertex edit mode, select the vertices where the boolean occured, weld at .01, then in the flyout window, hit "smooth" chk auto smooth and it'll wipe out those errors...or at least usually.
Hope this helps.