OK.
I think I've fixed the Battle of Bougainville, or at least found the faulty plane so I can start the mission.
The plane in my screenshot is a Mitsubishi G4M1-11 1941. One of them had their weapon loadout set to default. I changed it to match the others and the mission now starts just fine with me in a Wildcat on the deck of a carrier.
Thanks VPMedia for the explanation of that error message, and how to fix it.
Still can't fix the Doolittle raid problem. I've tried clearing and then setting again the takeoff waypoint (I tried it in an empty mission I started myself to see how it's done so I know it works for me) and even putting the planes over the carriers deck. All that happens is the plane I'm in spawns in the ocean or if the spawn point is on the carrier deck it blows up (presumably because it crashes into the deck).
Don't get what's up with that.
Also the black (or at least very dark) waters problem only seems to be an issue on certain 1C/Maddox maps, i.e. stock maps. Others seem to work fine, including addon maps (haven't noticed any that don't) and hardwaresharders are set to 1 in my conf.ini

EDIT - it seems I fixed it on maps like the stock Iwo Jima.
I found the following were set to 0 in the DirectX section of my conf.ini and I changed them so they are set to 1.
TexFlags.TexEnvCombine4NV=
TexFlags.TexEnvCombineDot3=
TexFlags.DepthClampNV=
TexFlags.SeparateSpecular=
TexFlags.TextureShaderNV=

Didn't have any effect outside of the FMB though, it still looks as dark in the mission when playing it as it does in my 1st screengrab.
Now, I'm supposedly running OpenGL, however I'm also using Reshade+SweetFx, which I understood to only work in DirectX, until I saw some people here saying they now have it working OpenGL.
Could it be that actually you end up running in DirectX mode, and therefore not in Perfect settings, by using Reshade+SweetFx with IL2 1946?