It is misaligned, but not by much. Just use the same procedure already mentioned but be willing to wiggle it around some and it should drop down that last bit.
Have a look here at the parts diagram (it's interactive so you can zoom in etc)
The rod locates in a bearing in the bottom part of the clutch cover and there's a notch in the shaft that locates it on a rod in the clutch assembly. Obviously it will till work if it's close enough, but you should be able to get it seated all the way down with a little patience.