If you still can't manage to manually stitch the extracted rectilinear
nadirs, from the horisontals and your nadir shot(s), by way of
photoshoping them together, you man want to try to stitch THOSE two
rectilinear views in PTGui, only optimizing your nadir shot. Output
also them as layered psd, and blend by using quick-masking.
If you'de like to "watch over someones shoulder" while they do the
entire stitching process (including nadir etc...), this too is
possible now, thanks to Eric Rougiers outstanding work with video
tutorials on this.
This is gonna save you a lot of trial-and-error learning time. Good
luck to you!