Your cannon and FLIR would be a different sort of problem, and without looking at the model, It is hard to know what the best answer is. In situations like that, I would probably first look to modify the mounting so that the parts could be installed after gluing the fusealge, filling, sanding, and painting.
If there is no way but to install the cannon and FLIR when the fuselage is assembled, doing some local prefinishing might be in order. Dry fit the fuselage, and if there is any major sanding and shaping needed around the cannon and FLIR, do it before assembly. You may even find it useful to use a coupl of drops of super glue to hold the fuselage halves together. The idea is to get the shape as perfect as possible, so that there will be a minimum of fuss to fill the seam after gluing for real. Before assemby, paint the area where the cannon and FLIR will mount. Assemble the fuselage. With luck, any parts of the seam that go under the cannon and FLIR are pretty good and will need only a bit of touch up, done carefully to not mess up the cannon and FLIR, and only minimally tweak the paint anound the seam. Now to touch up the fuselage paint, use a small brush, and a fairly thinned paint to alleviate and brush marks. At this point the cannon and FLIR should have good paint all the way underneath them, so any underneath coverage issues due to masking them become moot.
Andy