Looking at AA DC-4 photos, the windows do sit in a NM area. On other liveries I've done the following.
Paint the window stripe before installing the glass. Then install it, and mask over it. Then glue the fuse halves together etc.
I suppose a version of that which you might try would be to paint various panels on each side to include the area with all of the windows, install them and then mask those panels before final assembly, putty, paint.
I don't want to sidetrack the thread, but since we are on the subejct of windows: mine will have all of the cabin windows blanked out because it was a flying refridgerator.
References show the particular aircraft was a USAF C-54, which I would assume had windows. Then it went to Santa Fe Skyways, and the windows disappeared. After Santa Fe Skyways went under, the aircraft went through the typical downward trip of smaller aitlines, curious incidents (a hijacking) etc. where it got it's windows back.
In the SFS livery, theres a broad red stripe down each side, and the few photos I have from the railroad don't show an outline of windows in any obvious way.
So I wonder, since it was a non-pressurized a/c, was it simply rebuilt each time?