I only can try to imagine what you think of, cause both pictures are the same.
The base plate of the CP-2 is devided in 1/3 2/3 concerning the white mark on it. The position of the big yellow screw is the same.
You may mount it visa versa. I call this "long side to the lens, LSL, or short side to the lens, SSL".
The way you have to set up, depends on the upper rail setting you need for your camera lens combination. For example: if you need an upper rail set of 37 on NN5, it is SSL. If you need 132 on the NN5, it should be LSL.
For the NN3 you may use the following settings: SSL , you can use 96 to 32 upper rail settings with normal knob, 20 with small screw. LSL 106 to 52. To avoid to take the CP-2 apart taking panorama photos on the set, I have bought a second CP-2 and mounted them visa versa. Then I just change the different mounted sets if I need to change from SSL to LSL.
CP: Does not matter whether you mount it LSL or SSL because the reference point for the CP is the white mark in line with the yellow tripod mount screw. This does not change its position, whatever position you use. WHich side you have to mount to the lens is preset by your upper rail setting. Example: 50mm with D3 on NN5 needs 38, for this you have to mount it SSL.
To have a shorter site of the CP - 2:3 in length in reference to the yellow screw - offers you to set the camera to positions nearer to the ends of the rails.
So the question : Does my pano have bad quality because I used the "wrong position" of CP? NO!
LRS for D90 NN3 is 56, NN5 55. YOU have to check these settings with your own equipment, cause there might be small differences in the combinations.
18-105VR : first zoom, second UPS : 18 100, 24 94, 35 88, 50 78, 70 66, 105 29. For 105 you have to get another screw and replace the normal knob, which is too thick in diameter to reach this setting.
10.5 mm : 81, aperture 8, focus 0.5 set to aperture 8
If you like just send you photos and I will try to stitch.
To make sure that you are rotating the camera about the correct point, move the camera along the lower rail so that the centre of the lens is verticaly above the centre of rotation of the Nodal ninja, and move the upper rail so that the gold ring on your 10.5 mm lens is in line with the axis of rotation.
I have measured the point of rotation for a Nilon 18-200mm VR lens, which is 32mm back from the front rim of the lens.
I don't know how this compares with the 18-105mm lens, but it may be a good starting point.
I use a Nikon 10.5mm lens on a D60 and used one on a D300 last week and find that PTGui will usually give a good result with 8 horizontal images at 45° plus 2 zenith images at 90°, but have had trouble with this if there is a lack of detail in the common overlap between the set of 8 horizontal images and 2 zenith images.
To ensure I get a good result I now take 4 images with the camera tilted up by 45° or 50° at 90° intervals as well as the 8 horizontal images at 45°.
To reduce the "hole" at the nadir I sometimes tilt the camera down by 10° for the 8 images.