On some things, I had to go back and think, though I didn't edit. For example, tanks, really, can probably beat everything save artillery and other tanks. And maybe AT emplacements. And some dragons. Some. Infantry can probably beat the shit out of dragons(most of the time, all you need to protect yourself from breath attacks is a hazard suit. A high quality one, but still.); sniping you is easy when your head is the size of a car(shotguns if you get close; 12 gauge AD slug is pretty unlikely to miss)
Speaking of which, dragons should be small, and their scales should be tough, but nowhere near tank-like. Or Kevlar. Average length, I feel, might be around 20 to 30 feet. Too much larger thn that and physics starts crying about flying things and stuff like that. Some might be bigger, but unlikely to fly. Flying aircraft carriers are probably like bombers, and dragons will die if they get close, but fighters have a chance, and if bombers get overhead...that balloon can pop from a good sword swing. What's a bomb gonna do, ya think?
With water combat, I feel that it's a different field above and below water. Below, submarines are at a disadvantage. Not as maneuverable, not as accurate, far more vulnerable...of course, the dragon is basically going to have to stumble around until they see them with their eyes, as draconic hearing might be good..but it's not(usually) sonar. If the sub can get off some guided torpedoes or other AD weaponry, dragons gone. If the dragon finds the sub...sub's gone. Small, maneuverable boats above water with depth charges would work quite well against dragons though. Water carries explosions well, and there's a reason the term 'shooting fish in a barrel' was coined. The bullet hitting the water kills the fish from the vibrations.
Above water, dragons will take on an aerial role, or a submerged one; there's no reason for them to simply float. They could be boarding parties, for those with less than functional wings. Ships will probably be similar to modern ones anyway, though a bit faster and maneuverable with elemental dragon engineers. But the same anti air and heavy weapons, pretty much. PT boats will probably get into dogfights with dragons, since they can reach similar speeds, but dragons are more maneuverable higher up, while PT boats are more maneuverable close to the surface of the water.
On another note, dragons probably carry guns. Pretty fuckin' huge ones, too. They don't have our manual dexterity, and probably don't have the same aim, simply due to to skeletal structures, them being winged quadrupeds and all, but they can use them.
Finally, why 4000 years? It just seems so short, when dragons are involved. That's like...if we go with breeding age being about 70 for a dragon, barely 58 generations at the most. IRL, there's been (assuming average of 25 for generation) 4000 to get where we are.