When one side is higher than the other, sand!
When a seam is hard to reach,or is in a risky position to put blades or sandpaper, don't bother removing it! It most likely won't be very noticeable!
Or, in the case of your guns, try removing the seam before installing the guns, next time!
Finally, I always use putty. The only super glue I have, while not dangerous to plastic itself, creates fumes that melt, liquify, and warp plastic, so I try to avoid it like the plague! The putty I use is Testors Contour Putty. The stuff works miracles! I usually use it to add detail to small-scale hardpoints on my aircraft, or ammo belts for my Gundams. When I'm going to use it for seam filling, I try to use it much like an adhesive! First, I put down some model cement on part A, then I cover the cement with putty, then add a line of cement on top of the putty, and attach part B! Once it's dried, the bond is rock solid, and the contour putty has shrunk just enough that only light sanding will give you a perfectly seamless appearance!!