It looks like the lower is about the same distance from seating as the top. And it looks like the lower dust boot is making it look like its almost seated. Where the upper one looks like it has a long way to go.

That could just be the angle of the camera making me thing that.

 

Are you sure the upper ball joint is in all the way? Also be aware the upper joint is the "adjustment". That shaft goes in and out of it. It may be all the way in

 

There is enough thread showing in the pic that I think once you get to tightening stuff up it will all work out

 

Tome to get it done. I did that swap and was happy with the brakes. Eventually I put the Wj on the rear too