Is there a way to change the syntax colouring for spelling in TexWorks?
Currently red for comments and underlined red for mispelled words doesn't really stand out.
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Underlined text is hard coded by developers of TexWorks and cannot be changed.
As for the comments you can define your own rules for syntax highliting in a syntax-patterns.txt file in your TeXworks\configuration folder. After that you choose your syntax coloring from the top menu: Format -> Syntax Coloring.
This is an example of changing comments to blue. Add this to your syntax-patterns.txt file.
# comments black/cyan;I Y %.*
Here is a reference for more information.