You're right, it does fit... with enough "Cleco encouragement".
I had to de-cleco the bottom end of F-706 and F-707. Then I clecoed the vertical rib, F-730 spacer, F-706 and F-729A all together, got them in place and clecoed the assembly to F-706. Then I worked my way in from the outboard edges of F-706 and F-707, alternating every few rivet holes until I had both bulkheads clamped fully in place. At this point the rivet holes in F-729A did not line up with the holes in the belly skin, but with a little encouragement I was able to get it to line up and get all the clecos in.
I think I got spoiled by the empennage and wings. If something just wouldn't line up there, I just assumed I had it together wrong and that usually turned out to be the case. With the fuse it seems there's a fair chance it's just going to take a lot more work and patience to get it to line up right. This is going to be a long few months, I think.