Scotty,
The Polar Lights lighting kit is specifically for the TOS 1701 Enterprise. The 1701-A, or the Refit as a lot of Trekkies will call it, has completely different engine nacelles, so the spinning Bussard motors, etc, won't even fit nor would they be acurate.
There is a lighting kit specifically for the Refir kit, but I don't think Polar Lights/Round 2 makes one. There is a company called Tenacontrols that makes a lighting kit for the Refit. It has circuits for the deflector dish and photon launchers as well as all of the navigation strobes.
Tenacontrols also has a kit for the TOS 1701 that replaces the Round 2 lighting kit, although you won't get any clear parts like you would with the R2 kit. The Tenacontrols replaces the noisy motors with a circuit board that simulates the spinning Bussards.....way cool to see.
The stuff ain't cheap, though. I'm saving my pennies so I can get the Tenacontrols set-up. You'll probably need to research both lighting kits to get a clear idea idea of what you'll be facing. Check out SciFiModelAction 's website. There are tons of posts there dealing with both the TOS Enterprise and the Refit.
If you see a TOS kit with lit engine nacelles, it means the modeler decided to represent the original design of the studio model. The lit nacelles were axed by the studio due to the added expense. The 1701-A, which first appeared in the first studio movie, HAD lit engine nacelles.
Hope I didn't create any more confusion for you.
Matt