It seems that the common component in most of these FCR threads with fitting issues is the manifolds. Just throwing this out there, but it looks like these manifolds are intended for the bonneville type bikes and the angles are not quite right.
So have you looked at altering the manifold to correct the fit issue? From the pictures it looks like your carbs are both higher and farther back then where mine are with the stock manifolds.

05 speedmaster - 1100cc, 11:1 racing pistons, Carillo rods, thunderbike cams, ported and polished head, 2mm over intake and exhaust valves, Barnett kevlar clutch, scepter pipes, oversize manifolds, 45mm HSR's, TTP stage 4 firestarter