You really are treading a well worn path.
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.
Aussie Ninja