I'm left wondering why the cv-axle dust seal got pushed away from the rear of the spindle assembly in the first place. With the hub assembly removed, there should be nothing to obstruct the cv-axle assembly from mating back up to the spindle assembly.

Once those two assemblies are mated completely with no gap remaining like you were first experiencing, I remember having to spin my hub assembly as I was putting it back on to get it onto the spindle assembly as far as it would go, and at that point (and after using the hub nut tool to set the preload), sliding the hub flange onto the axle splines and spinning the hub until the bolt holes lined up. IIRC that is, it's been a long time since I replaced my front bearings too.