i think Chaz is right, it will/may always be out of alignment with(out) the missing spoke. Too bad the rag joint (i'm assuming} is all mounted up, that spoke would be EZ to replace before the sprocket was mounted. If it is some other kind of mount perhaps the spoke can be replaced in situ.
Crassius too is correct, and if it is a rag joint, the bolts on one side may be tighter than the other, making the plane of the sprocket tilted in relation to the plane of the rim. That popping sound, BTW, will likely soon be followed by a chain link being pushed apart.
In my later builds i have been loosening the spokes a little before i install the rag joint. It allows me to move the spokes out of the way for the bolts, and i ususally wind up having to true the rim anyway after cranking down the sprocket joint etc. That sprocket and joint puts a lot of new, weird pressure on the spokes.
I made a tool to help with the "concentric" aspect of mounting. It does not prevent the sprocket from being off center but is more like a gauge or measuring tool. If you lift it out and it binds, the sprocket is not centered. But this allows me to concentrate on the "tipping" aspect which i both eyeball and use a block clamped to the chainstay to "measure"