Menu arrangement is currently the way it is to be consistent with similar applications.  Actually, if you look back at very early versions of Simply Fortran, the Help menu was way over on the right like you've suggested.  However, this placement did actually cause confusion.  Additionally, if you look at many common menu-based windows programs, many, including those by Microsoft, no longer push the Help menu to the far right. 

As far as swapping the Project menu and the Edit Menu, that issue is certainly open to discussion.  Again, it's placement is just for consistency with similar programs, although Simply Fortran doesn't necessarily seek to be a clone of anything in particular.  If others feel it would be more efficient, it can certainly be moved.

The ones I use nearly all the time are, <Project> and <Options>.
I'm not so dull-headed that this takes any significant amount of time, but it nevertheless breaks my rhythm a little.
I wonder how anyone else feels about this because my feeling is that, if the menus were in this order, the program would be a tiny bit slicker to use:

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File   Project   Edit   Build    Toolbox   Options                                                            Help

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John