Steve is right.  This can be a lengthy, but very rewarding project.  The Detail and Scale book is really a "must have" if you want to take the time to improve the Tamiya kit.  
The differences would of course never be noticed by the casual observer, so it's totally up to each individual just how much extra lengths they want to go to.  But I know that once I start looking at the photos and comparing them to the kit, I can't stop myself from getting out the sheet styrene and trying to make the kit actually look like the real ship. 
As far as the air wing goes, if you decide to make the ship look like what's in the detail and scale photos, it puts you in a somewhat narrow window for what wing and squadrons are, if you choose to go for historical accuracy. The book shows Enterprise the way she looked after her major overhaul which started in 1979, and before her next major re-fit which started in 1990.  During that period, CVW-11 was the wing that always deployed with her, and the composition was pretty much the same.  That is VF-114, VF-213 (F-14A), VA-22, VA-94 (A-7E), VA-95 (A-6E and KA-6D),  VAW-117 (E-2C), VAQ-113 (EA-6B), HS-6 (SH-3H), and VS-21 (S-3A)
The only difference is that from May 1984 through Jan 1986, VS-33 was the S-3 suadrron instead of VS-21, and starting in October 1987, VAQ-135 replaced VAQ-133 as the EA-6B squadron.  
As far as painting goes, it's hard to get real precise.  During this period most squadrons first went to overall light gull gray (FS 36440)  and gradually replaced colored markings with gray and black.  Then the "official" tactical 3 color scheme came in which was a combination of FS 35237 on the tops and FS 36375 on the bottom with FS 36320 on the sides! This scheme was supposed to not have any colored markings, but reference photos seem to make it clear that not everyone followed the rules.
If you're going to use the aftermarket decals, I'd probably just paint everything with the light gull gray and used the low viz rather than the color for the markings.   
And if you're planning on doing a complete air wing, I can let you know the side numbers that each squadron used for aircraft in the squadron.
Tom