I recently went through the same problem, except mine was worse, I rotated the starter 180 to clear my headers.
What I ended up doing is using a 1/4" drive and two flexible joints, and some sticky stuff in the socket. Believe it or not, with a really stong flashlight, you can see where there is room to get to the top nut from the bottom and inside the tranny tunnel. I think I also ground down a bargain-bin spanner for the top. I now have three or four highly modified tools for just one application somewhere on the car. I keep them in a small box with labels so I will remember. I sometimes forget what I had for breakfast. Of course, taking the tunnel out and the bolt goes in in 12 seconds. It ain't that bad, like changing the rear sparkplug on my old rat motor Vette, a friggin nightmare....
Bill