How do you get FDM parts to match resin parts on a big model?

That gap you see is almost certainly related to the difference in material shrinkage and resolution between FDM and resin printing. When you scale parts, you are scaling them based on the original 3D model dimensions, but the way those two materials expand or contract during the build process is unique. The quick way to fix this without modeling fillers is to use a test print on one of the smaller components that joins the hull. Print a test version of the cannon and the hull port, then measure the gap between the two physical objects with calipers. If the gap is too wide, you need to adjust the resin model in your slicer, scaling it down slightly untill the physical measurements match the hull port. If the resin piece is too tight, scale it up. Don't worry about guessing; just measure and adjust until the fit is clean. Because the resin parts are smaller and more detailed, this kind of fine calibration is more critical than it is for the main structure. Regarding the materials themselves, regular CA glue should work fine for mixing FDM and resin. Since you are dealing with a hobby project and not structural engineering, a standard cyanoacrylate adhesive like Moment or Krazy Glue is ussually the go-to method for this kind of assembly. You just want somethig fast that bonds securely without being overly bulky. There is no need to model custom filler pieces for every single joint. You only need to adjust the individual parts that are causing the interference. It’s a tedious little measurement dance, but once you figure out the required offset for the resin prints, you should be good to go with your accessory runs.

Been doing hybrid builds since the days we were hacking apart FDM parts with a hobby knife to make room for resin bits, and the one-cannon test print is the right call. Just do one, dry fit, tweak, repeat. Took me three tries on a galleon once and I stopped trusting slicer numbers after that. For the glue, CA works fine on clean, cured parts, but if you end up with a gap anyway, a dab of two-part epoxy or even spot of putty fills it and gives you some working time to line things up. CA grabs fast and gives you zero second chances once it bites.

I'd push back on blaming material shrinkage here. Cured resin barely changes size at all, and the OP said the resin parts feel oversized, which is the opposite of resin shrinking. What actualy bites you is the FDM side, small holes come out undersized on filament printers because the outline squishes inward, so the ports on that hull are probly tighter than the model says. Measure the port itself before touching the resin scale. Also secondhand machine, worth running a quick calibration cube first because if it's off, every tweak you make to one part is wasted on the next batch.

Kind of relieved to see this thread because I ran into the same headache making model railway buildings, resin windows into FDM walls. What ended up working better than rescaling was just opening the holes slightly with a needle file until the parts dropped in. FDM holes always seem to come out a hair tight no matter what the slicer says. Wondering if that'd work for cannon barrels too, or if round ports are harder to touch up than square window openings?