Maybe I could help a little here after fixing quite a lot of common damage issues in many planes.
I'd recommend as first step to look at meshes of some other plane, preferably the one your Java code is based on. There I assume that all the damage code of that plane is in classfiles of your plane also and should thus work fine when you fix meshes with proper collisions named like in that other plane. Hopefully that plane is similar enough with floats instead of wheels and radial engine without water radiators, but even with very different base plane most of the damage code should still work fine.
Then you should try to add proper collision boxes or hitboxes for D0 meshes (section starting with [CoCommon]). You can check naming from that other plane and just modify shape and position of collision boxes to match your 3D model properly. After you think you've successfully exported D0 mesh with those hitboxes, then copy that mesh as D1 with different material and again as D2 and D3 with different material so that you can test damage in game after adding those damage meshes to hier.him. You can just copy material files, names and damage textures from that other plane for testing, but eventually you'll need proper damage textures and you can start adding internal structures and alpha holes in default skin to reveal them if you want very nice visual damage. I recommend spawning E15K on airfield behind your friendly bomber and shooting it with bomber's rear gun to test damage. If your damage doesn't work properly up to complete destruction of that part, then check first that D1, D2 and D3 meshes have similar hitboxes to D0 mesh and vertices of those hitboxes aren't flipped to face inwards. Hitbox names are also case sensitive and I've fixed some planes with broken damage due to mismatch there.
Then you can consider adding CAP meshes after you get hitboxes working fine and parts detaching by shooting them thanks to proper "Separable" lines in hier.him. Collision with ground is completely different system and only based on "_Clip" hooks instead of hitboxes.