custom upper is big bucks, especially since you have to be careful and not have ones that disperse the a/f mixture unevenly. You could maybe fab up a connector plate/tube setup that merges the 2 tb's into 1 outlet tube that mates up to your upper, but that would lead to even more clearance issues, unless it extended a decent amount away from your upper and repositioned the TB's near the fender.
The only question in that setup would be if there is a minimum distance that the TB should be away from the upper intake manifold, or could it be extended out 10 or so inches and connected via a 75mm tube or whatever your upper would accept. My assumption would be that it would lead to a possible bog point for air, but once again, all speculation.