Besides removing the 1-1/4" axle nut and clamp on the CV boot, remove the three lower bolts/nuts for the ball joint that attach it to the control arm, and the two lower bolts on the strut. This will allow the strut to swing out enough to get the end of the axle shaft out of the wheel bearing.
To remove the inner CV companion flange you would have to take out the right side carrier bearing bracket(right rear motor mount) you can leave the intermediate shaft in place.
There is a large snap ring on the transmission side of the bracket that holds the companion flange shaft in place through the bearings. The cover for the intermediate shaft covers it up IIRC.
It can be done without pulling the engine - did that when I converted my 9000 from Auto to 5-speed.