I find it a really useful and excellent way of stitching using John's way of stitching by use of masking out what i do not need on the nadir then feeding all images into PUTgui but recently, i've change my gear a bit and trying out some compact camera pano shooting and i hope to be able to overcome this.
i'm sorry, i would like to stick to John's method for now as editing the nadir seperately has always given me less than ideal nadir (eg different tones/ shades or colors even with the exact same camera aperture/ISO/shutter) but with his method, i have achieve perfect nadir all the time except the appearances of the lower rail of the NN3.
Compact Nikon cameras work somewhat differently to the way Nikon DSLR camera work as far as the AE Lock is concerned. (At least they were up through the earlier Coolpix range)
My memory on this is being tested as this comes for experiences from many years ago. In fact back to the late '90's. Searching older forum archives should find you many answers on this. Try the Easypano Panoweaver forums.
Basically, You should set your camera into Manual Mode, Set the Aperture to f/8.0, Set the focus to Infinity (looks like mountains ^[size=14pt]^[/size]), Using the internal light meter adjust your exposure shutter speed to match the centre mark of the EV meter (looks a little like -EV|--[glow=green,2,300]|[/glow]--|+EV) this meter reading and shutter speed adjustment should be taken based on the most even light of your scene. Older and I guess newer Coolpix cameras did not cope well with higher ISO settings so sticking to ISO 50 or ISO 100 will be best. To keep the Coolpix panorama images at the same colour and exposure etc you should now lock the Automatic Exposure (AE-L) and reset it after shooting each "set" of panorama images.
The issue you are having capturing the forward section of the Nodal Ninja lower rail and bubble level is due to the design. (Basically it wasn't designed for this job) This is not the case with the Nodal Ninja 180 panohead and would be well suited to what you are wanting to do. To get around your issue you would be best served to shoot a nadir shot off panohead - hand held and use PTGui Software "Viewpoint" correction feature to stitch in the nadir image.
Thanks again AN. I retried once again using back the upper arm, it works great with the settings you posted using an image on the other thread. Guess i have to stick to the upper and lower arm for the NN3 to avoid this problem as elevating the camera on the lower arm seems to work but if elevation needs to be that high, it defeats the purpose of having a lightweight kit such as the one i am trying (no upper arm). Let's wait for the NN 180 then!
Your suggestions on the AE lock, i'll look into it soon. Have been neglecting my dSLR for the past few days trying to get this light weight pano kit to work well. oh and i am on Canon system but what you describe is of course, still very valid on the EV metering.
The Coolpix cams, P5100 i am using has it's limitations but nonetheless, it's quite a handy and good camera. The noise at ISO 400 is unbearable and could have been i have always been a Canon user thus the bias at certain settings. I use both systems now i guess so to each it's own. It's the fun i am having and trying out these equipment on different settings and the people i meet and learn from along the way that really counts for me.