Jason - I think Jeff is correct about the intake, I don't think it is possible.
I personally believe your problem lies in the using a two-barrel on a one-barrel manifold, not in the orientation. We have seen these things mounted correctly, backwards, and to the side on various street applications (and some race applications) with no problems.
However, if you want to change the orientation, the bowl would have been to the front.
As far as linkage is concerned, it is very easy to change linkage motion 90 degrees:
(A) Visualize a capital letter "L" with equal length legs.
(B) Drill 3 holes in the "L"; one at the "heel" of the L, and one at the end of each leg.
(C) Fit the L over a stud using the hole at the heel.
(D) attach a linkage rod to the holes in each leg
(E) when the L rotates on the stud, the linkage motion is now changed by 90 degrees.
Personally believe this will be a waste of time, but it is fairly easy, and if you have the time, it will allow you to correctly orient the carburetor, and prove what happens one way or the other.
Jon.
