You only need 6-around - that probably explains some of your problems; excessive overlap.
What pano head are you using?
When I shoot with my D40 and Nikkor 10.5mm FE - I shoot 6-around at -10 degrees pitch and 1-up at about +65 degrees picth.
These image sets usually stitch very easily with APP - use APP 1.4.2 because the alpha is not stable and has some major control point detection issues at this stage of development..
This will give you good zenith coverage and only leave a small 'hole' at the nadir.
Give it a try.
Now I've seen your images, I see you have vast areas of relatively featureless pale coloured walls, ceiling and floors - such scenes will always be difficult for APP's automatic control point (CP) detection system. Some people recommend placing 'targets' around the room with such scenes to provide some distinctive features to help the stitcher (or the user) to place CPs, and then to edit them out of the stitched pano image afterwards.
You need to turn all the lights on too!
And use the same fixed manual exposure for all shots. And use a smaller aperture - say something like F6-8.
Did you use flash? - it looks like it becasue of the severe vignetting (light fall off at the edges of the images) and that's a real 'no no'.
1. This is a difficult scene to shoot at the best of times. If you are new to panoramic imaging I recommend to practise a bit with easier scenes - outdoors in good light, scenes with lots of features - before trying to tackle indoor scenes such as this one.
2. Your shooting technique is all wrong.
3. I don't believe it is possible to generate a decent pano from this set of images - so I suggest you forget about trying to and start again. See below for the best I could do after a lot of (unjustifiable) fiddling about.
If you would like some image sets shot with various cameras and lenses to practice stitching you'll find some here - they are nothing special and far from perfectly shot but will serve the purpose: http://www.three60views.org.uk