After giving it a couple of days of thought I decided to drill the J-channels to the aft ends of the side skins without the F-779 bottom tail skin in place, so I could use clecos through the whole assembly to align the parts and avoid figure-eight holes in the F-779 bottom tail skin. I backed up that decision with some research on VAF and found several builders who had done the same thing with positive results.
Photo 1 shows the best alignment between the F-779 and F-773 I could get without being able to use clecos to wedge the 779 into position. Photo 2 shows the F-779 removed and the J-channel centerline centered in the F-773 side skin holes. Photo 3 shows that I only marked the holes in the J-channels with the drill at the bulkhead to prevent figure-eighting the most likely misaligned bulkhead flange holes. I'll finish these holes off the airplane.
Note: I used a 3/32 drill instead of the slightly larger #40 to help ensure alignment when drilling the assembly.
Misalignment between the F-779 and F-773.
F-779 removed allowing access for drilling the J-channel underneath.