Paul
I have had a number of planes with twin FAAST receivers installed. Never had any issues with them. Never had a problem with the receivers being positioned like you have. Using twin receivers gives you the opportunity to have the uncovered ends of the coax wire orientated in different directions. The ends should as you say, be at 90 deg from each other. You can now get 3 axis reception with one pointing up, one pointing to the front and one to the side.
John