Did he jefferies intend to have anything going on there?
It depends. There are some sketches when he's working out the new "power pods" and he indicates a glow on the top of the new nacelle caps. Those caps, however, are a different style than what was ultimately decided up.
There was also a note that he only intended to suggest a change to the nacelle and struts, and not to the rest of the ship, although in reality subtle alterations would exist.
We also know from seeing photos of the incomplete VFX scale model that there is only a solid mass on the front of the nacelle caps.
On the deflector dish, I asked Andy Probert on this board once and he replied he had no memory of anything special planned for the Phase II version such as a lighted deflector. The working sketches I've seen all indicate Jefferies planned to keep a classic TOS deflector dish. Why it isn't indicated on the finalized plans or schematics is a mystery.
Dennis, what Mike Minor images are you using? Are they online?
(Bless you for using purple and not the blue.)