Hi,
I think that the problem here with the discolouration is that there are two bodies on
top of each other. It is probably the fuselage and the window trying to be displayed
at the same time.
Another method that you may be able to use here might be a Combine Intersect to get
rid of this.

My cutout of the windows does not overlap like yours does so I am not sure
exactly what you have done. If you do have two bodies overlapping then what
you want to do is use the Combine Tool but use the Intersect switch so that the
body that remains afterwards is the one that intersected BOTH bodies which is
where your problem is.

In this case you will probably want a new component and keep tools.
I don't see any issues with achieving what you want, it is just a matter
of setting it up right. In this case, I would probably cut the window and
the frame as separate bodies and depending on what you want to do with
the model maybe set them up as components. I would modify the
appearances and either use Group or joints to join them together. Then you
should be able to use the linear Pattern to make your row of windows.
If you get a bunch of fuselage patterns copied then you are selecting the
incorrect bodies for your pattern. Also don't forget that fusion has a few
issues with choosing what to call new bodies after they have been split off
another body. Sometimes the parent body remain and the new body is Body X,
and sometimes the new body is the Parent and the old one becomes Body X.
It is very frustrating not being able to choose sometimes. This may be simply
a naming issue not a component issue.
How would I model instead of the forms? Probably with Lofts and the other tools.
For example, one of my first aircraft models was a Lockheed 1011. You modeled
the Wing Box with a Form, I achieved the same end result with an extrusion for the
main box and lofts to get the curves right on each end and blend with the fuselage.
Looked exactly like my 3-view canvases. That is not to say you did it wrong. There
are many ways to achieve the same end result in fusion, you just did it different.
One of the things that I have learned along the way is to try to keep my designs as
logical and well set out as possible. To do this I work as if I was part of an engineering
team and my work has to fit in with the rest of the team and also has to be readable
and reproducible if I left the team. I am a student engineer and I don't know it all but
this seems to work. I will find out when I join a real team of engineers.
To help me I will also try to create as much of the framework of my design before I start
designing. I am currently working on several projects at the moment but one of them
is a simple one cylinder diesel engine (I have a book on engine design and I am not afraid
to use it 😎). I have not started to draw anything yet but there are several Assemblies and
sub-Assemblies that I know will be part of my design. What I have done is simply create
these assemblies and sub-assemblies ahead of time so that everything is logical.

Now this is not nearly a complete design but it is a good framework and has much of what
I will have to do later already created. I know that I will need to add Components, Assemblies
and sub-assemblies later but it sets the framework so it is easy to do this. By manipulating the
timeline, when I am ready to create a new part I can simply come back to the beginning and
create the Component as if I did it at the start and nobody will be the wiser and everything
will remain nice and clean.
In terms of the wing. Three different lofts were not necessary. You have the profiles to use as
Loft Gates and the Rails so just do it all at once. The whole point of the loft is that it will modify
itself to the different sizes and shapes as it generates from one gate to the next. The L-1011 model
that I did also had different airfoils. The two inboard were identical just different sizes but the
outboard one was a different airfoil AND had a 4 degree twist. Loft coped exactly as expected
after it was set up correctly.
In terms of what the model will be used for this is a great first attempt. If you want to learn more
about Fusion then see RULE #0 that is usually Pinned to the top of the forum. I regularly model
stuff I am interested in just for fun and to learn new techniques. I am also currently doing a job
for someone where I am designing a Ducted Fan. I have learned a great deal about practical
aerodynamics (I already know the theory) and also a great deal about modelling with this design.
Practice makes Perfect. Keep modelling stuff that interests you to get better.
Cheers
Andrew