On round gear machines, there is merit to doing wheel pants, gear leg fairings, and intersection fairings at the same time, in flight configuration, level, and gear unloaded.
This allows you to treat these as a system and use the alignment tools, tape on the floor, plumb bobs, string, and tape measure in my day. (This all would be much easier with a laser, but same concept).
The risk of doing this with the gear loaded is you may introduce yaw, or excess drag, in one or more of the parts.
I would take Larry up on his article.