Glass cloth on the center section of the wing around the entire joint (top and bottom) had no effect on the alignment.  I used masking tape on the wing so that the glass cloth and epoxy was on the inside of the glue joint.  Once the epoxy dries I sand the edge of the masking tape to remove it.  I use a level on the nose of the plane (on the SV-11, this area is parallel with the thrust line) to ensure it is in fact level and in a stable position so it won't move, and I use incidence meters (old mechanical ones made by Great Planes, they also make laser meters but I have not used them) on the wing and tail.  I tack glue things in place with CA before final gluing.  I hope this adequately answers you question.

Don

I set the plane on the landing gear with the tail on a small box and shim it with some balsa until its level. I did not have the flaps installed at this point. You can do it with the flaps installed, but it becomes more difficult to get the incidence meter in place and a slight movement of the flaps causes a deflection in incidence.  Once I get the wing glued in place I do the stabilizer the same way.  I also found that both of the ARF SV-11's I put together did not need much adjusting other than a bit of sanding to get the stabilizer level.  As a side note, I usually glue the flaps and elevators on as the final step in the build, because I normally scratch build and paint. This way the hinges don't get gummed up with paint.

Don