I think I built that kit a long, long time ago... anyway, I have had similar problems with some F-14 kits. I would say that you strategy depends on the severity of the gap. I usually use a gap filling super glue like Zap-a-Gap with an accelorator to fill gaps. If it is a gap on the order of a 1/16th of an inch or more, I would first try some putty. Putty seems to fill large gaps better. Use a toothpic or something to apply it in the tight spots between the intakes and the fuselage. I would still recommend using superglue to seal in the putty after it has been sanded to shape. The trick with using glue in your situation is not getting it all over the other parts in the area. Again, a toothpick or other applicator will help.
You can buy some sanding tools that will aid in the sanding process. There are some tools that use thin strips of sandpaper on a handle (similar to the way a coping saw looks, but with sandpaper instead of a saw blade). Some small files can get into the tight spots too. And if all else fails, I just roll up some larger sheets of sand paper into the shape I need and just hope it conforms to the surface without doing too much damage to the surrounding areas.
I would say just give anything a shot and if it ends up really bad... there is one more reason to go out and buy a new kit to improve on.