One more idea about using a laser collimator (possibly already thought of and used). Once you have aligned the focuser (I proposed a hole in the other side of the tube), replace the secondary system and remove the primary. (This will only work for tube scopes)... Make a big Vee block arrangment which will take the whole scope. Probably need some kind of roller points for friction. With the laser in place, rotate the whole scope tube in the Vee support and observe the laser spot on a distant wall. It should circumscribe a small circle whose radius is the secondar offset. Ideally this should be done a two distances to really assure that you have a beam parallel and slightly offset from the main axis of the tube. Basically the same procedure you use to align the laser in its housing. Note I have not tried this yet so caveat emptor.
Steve