The answer on the airplanes is ... it depends. I know that's not what you wanted to hear, and I don't have specific knowledge of the Tamiya kit, but - which aircraft are "correct" for your Big E depends on what time period you are building her for. If it's the present day, then the flight deck is going to be filled mostly with the smaller F/A-18 Hornets and a few of the larger Hawkeyes, Prowlers and maybe a Viking or two. Plus the SH-60 helos, which are smaller than earlier types. If you want to do it from 5-10 years ago, then the F-14 Tomcats, much larger than the Hornets, will be the dominant airplane.
But hey, it's your model, so pick what you think looks the best!
As far as the deck seam, all I can suggest is careful sanding and dry fitting before gluing down, and using masking tape on each side of the seams before you apply putty or filler, to save as much of the deck detail as possible when you sand down the seams.