I'd forget Watcom: FTN95 is much better and more up to date.
All valid Fortran 77 code compiles straightaway with FTN95, and the bits that don't are often library functions that FTN95 has in some form or other - graphics are a case in point. The first part of a project like yours is to gain familiarity with FTN95 and get to the point where your application compiles and runs as a console application (i.e. as it did under DOS). You won't get DOS graphics, but everything else should be practical. If you try to convert a non-running application you just make life difficult for yourself!
It is highly likely that what you thought was a great user interface under DOS was actually fairly primitive, and is at the least sophisticated end of the scale just a way of specifying input & output file names, with the input data file containing simple lists of numbers. At the most sophisticated end of the scale, it will have data input 'screens' that are rigidly defined. Duplicating the former in Windows is trivial, and duplicating the latter will not satisfy you - it will look primitive!
It is entirely possible to use the Clearwin+ functionality in FTN95 to create a system for inputting information into datafiles, and editing datafiles, but this is usually not a trivial exercise, and you would be well advised to sit and think long and hard about how you want this part of your program to look and operate before you start, especially if you want graphical interaction. Presenting results is much simpler. The analysis 'guts' of your original program will eventually form a few subroutines in this Windows program.
You can do it as a Win32 program or in Visual Studio, but I suggest the former unless you come at this as an experienced programmer in Windows and languages other than Fortran.
For someone with a background in Fortran and nothing else there is no better solution.
Getting some direct instruction in the niceties of Clearwin+ can give you a headstart, as the documentation isn't a self-instruction text. If you are anywhere within easy reach of the area SW of London I could offer volunteer help, but it does depend on where you are based.
Eddie