HI LIddleMaus, I like your choice of model, and also your aproach with spline modelling.
About the issue when making the wing root, twisting some polys from the side of fuselage:
maybe things will look better if you assign to the polys being the root and future new wing, a different smoothing group than the fuselage part (probably much better with a couple of them, depending on your choice).
Otherwise everything will have the same one smoothing group, and things will look just wrong. (specially in wings, or control surfaces, with two opposite surfaces, but there are many situtations when this happens)
polys in the same smoothing group share the same lighting at render time, as if they were receiving light from the same spot. So you have to be aware of this effect sometimes and assign different smoothing groups to some areas to make them look and render right.
In the case of wings, if they are integrated in the same mesh than fuselage, generally they look better when they are put on a different smoothing group than the fuselage, normally starting with the wing fairing.
Smoothing groups are also used to visually separate some features of a model, like fairings, bulges or raised areas or parts made of different materials like glass/canvas/metal/wood. You will find this very helpful when modelling some areas.
As HundertzehnGustav rightly pointed, as alternative to the "twisting", in many examples wings are made like a separate mesh that just goes through the surface of the fuselage side without actually being joined with it. In this case, smoothings groups are not an issue, normally. Also you can save some polys doing it this way.
Personally, when I face this situation, even if I start with separated meshes, I prefer to integrate wing root with fuselage in the same mesh at some stage, and put the vertices where I want them.
As you have some profiles for the wing made of splines, maybe you want to try another aproach.
there's a tool that projects a spline onto a mesh cutting the edges on it like if you were drawing the shape on its surface. Going from the top of my head, it's called "compound shape" or something similar and is located under the "compound objects" in the right rollout (you will need to unfold the type of primitives menu, to see the option)
*Edited: It's called ShapeMerge, not compound shape! I'm sorry--> too few working brain cells...* basically, you choose the spline (the nearest to the fuselage), then the mesh, and voila! you have your mesh cutted with the projection of the spline. Be sure to make a copy of your mesh first, just in case, and work with the copy. Add a Edit Poly modifier after the compound object, and then you can select the polys than form the new "cutted" area and extrude those, or whatever you want to do with them to form the base of your wing root.
The downside of this is that some surplus vertices are created along the lines of the new edges and you will need to delete them. Also these new vertices are not conected with edges to the rest of the mesh, so you'll have to connect them. (My explanations probably make that cleaning step look more complicated than actually is...)
For lining-up vertices, the snap otion is your friend. You can set its options to snap only vertices, set the ignore backfacing option when doing this, in the vertices level of your mesh, and uncheck the backface culling in the display properties tab.
In modelling software there's always different ways of doing the same thing so don't discourage you if things go south sometimes, and keep trying when you recover the right mood. Sure you'll find some way.
Finally, as a personal advice, have you considered to use a symmetry modifier at some point? maybe it would save you from repeating some tasks and keep you safe from some mistakes. I hope this helps, keep going and good luck with your project.
No need to say, you are forbidden to give up!