Ken,
The rear window section (bottom bow) did not chick (lock) in the upright position before you stowed away the top into the boot. What is happening is that since the rear section was not locked before placing into the boot, it is moving backwards as you try to raise the top out of the boot and will not clear the boot. When bow is locked, it will not move back and will come up with the rest of the top bows. Only thing you can do is get two people on each side of top to very carefully work the top out. You will rub the top, but only way to get out of boot. You may want to try to get your hand on the bottom of top at the bottom bow to lift. This will force the bottom bow to stay in a locked position. Not a lot of room to work in.
I think that we have all experienced this problem when we first got our SLs. Helps to read directions first. Also you might want to see if you have the "O" springs at the main footings of the top. These could be missing or week, which will cause the bottom bow not to lock in the upright position.
Bob