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Looking at the docs, I can see that one of the files that is required for WinQuake but not included is wdirnop.pif, is it necessary or not?
This question / problem has been solved by Voodoo84image
Not really. PIFs (program information files) are kind of Windows shortcuts to MS-DOS programs, but unlike regular shortcuts, they also describe additional parameters required to properly run targeted DOS program in Windows environment (amount and type of RAM, full-screen or windowed execution etc).

PIFs were relevant back in Windows 95/98 days when Windows could run DOS programs. Newer Windows based on NT technology (anything from Win2000 onwards) can't run DOS programs anyway, so PIFs are not important anymore.