Depending on the space in your workshop it may be best to leave the longtitudinal rack tubes till the end of your build, it is much eisier to get in to work on the cockpit and bottom of the boat if they are out of the way, and the boat takes up much less space.
I will also echo Phil's comment about lining up the racks, they can look very different when on the water compared with on shore, and the slightest mismatch becomes obvious.