The CV joint allows the axle to extend/contract as the suspension moves up and down. I believe if you push inward on the hub, you'll find that everything moves back in where it belongs.

You may find that the new control arm bushings make it difficult to pull down on control arm enough to slip the ball joint back into it. If that's the case, try leaving the control arm mounting bolts a bit loose until after the ball joint is in place. If that still doesn't help enough, here's something that worked for me...
I hung a large (maybe 5 or 6 inch) C-clamp over the leading edge of the lower control arm. Then I slid a 2 or 3 foot long pipe through the C-clamp and rested the end under the subframe. That gave me a lot of mechanical advantage to pull the control arm downward by prying down on the outboard end of the pipe. Then just be careful not to pinch your fingers when you slip the ball joint into the control arm and release pry bar.