I built the Buzz Aldrin Saturn V kit about six months ago and had a similar experience, although from the sound of it, not quite as bad. In my case, it was only Stage II that had a significant mismatch, Stage I and III were pretty close and didn't require much tweaking.
For Stage II, one of the halves was maybe 2 mm shorter in radius than the other half, such that, when aligning one side perfectly, the other would not join together evenly.
The first thing I did was to gently flex the two halves to make them closer together in size. So, I would flex the larger half inward, and the smaller half outward, until the difference between them was reduced to a more workable level. This took a while, in several sessions. It's sort of a miindless activity so you can do it while watching TV. Just be careful not to flex too much and break one of them in half! Anyway, this got me to a point where I could at least cement them together and get the edges to look reasonably even with only a small amount of gap showing in a few places.
Next, to fill in the gap and cover the seam, I used several applications of Elmer's White Glue. Spread it on liberally into the seam, let it dry and then wipe off the excess. The beauty of this was that since the rocket itself is painted in flat white, the glue blends in perfectly as is and you don't notice it at all. Of course, if it does show, you can always just re-airbrush or repaint over the seams in your base color and it will disappear.