Well, after spending a bit more time between my Mavericks system and my El Capitan system, I finally have been able to get ViewNX-i and CaptureNX-D working in El Capitan. ViewNX-i is Nikon's newer supported version of ViewNX 2 and has replaced it as such.
In order to get these to work in El Capitan I made sure they were working in Mavericks and then proceeded to copy the Nikon folder inside 'Applications' on Mavericks and then placed it into the 'Applications' folder on El Capitan. The next step I needed to do was copy the Nikon folder located in 'Library/Application Support' on Mavericks and place it into the 'Library/Application Support' folder on El Capitan.
That is as easy as it gets. After doing this I tried loading ViewNX-i in El Capitan and it loaded fine and worked without a problem. I then tried CaptureNX-D and it also worked fine. So they work fine once they are resident in the system properly. I'm sure ViewNX 2 will probably work doing the same thing but I am using ViewNX-i now so I won't try it.
The problem with installing the Nikon software with Nikon's installer is the installer itself. I'm sure it has to do with Apple redesigning EL Capitan's USB support. Nikon needs to redesign the installer to work with El Capitan, but for now this is a work around.
Hope everyone can follow this so you can carry on using El Capitan with Nikon software.