As far as clearing the lower ball joint, Try sliding the spindle into place and see if that doesn't help. Every dana 44 I do always seems like the shaft isn't gonna clear the lower joint but when you put the spindle on it centers everything up.
The upper ball joint should have come with a small cap to screw into the grease fitting hole after you fill it with grease.
To get the upper joint tight try putting your jack under the lower joint and jack straight up so that it presses the taper into place. Of if you have the tool get the lower joint tight and tighten the upper adjuster down.
