The bottom hole is used for the red Koni shocks. The top hole is used for the double action silver Koni shocks. Front and back. Which also must be installed with the body down. This was discussed on the other forum and confirmed with a call to Factory Five. Looks like you have them installed that way, so all good.
Thanks. i contacted Tech and go this answer also.
Unfortunately, your UCA's are installed incorrectly. The rear pivots should be on the top, and the zerks pointed up. The pictures in the instruction manual show it correctly, but unfortunately it's never mentioned that it's necessary to disassemble and re-assemble to get the proper orientation. You're in good company. Many have missed this. They come from the vendor assembled upside down for this application. Your upper ball joint is installed correctly, with the ball joint pointed out.
Note: While you're fixing this, it's generally recommend to have bolts go in from the top with the nut on the bottom. That way should the nut ever fall off, there's a chance the bolt will stay in place and avert an even worse situation. When you take the UCA's apart to flip the pivots over, put the bolts in from the other side.