Although the edit menu is a bit obsolete, and for setting up complete positions I would expect almost everyone to paste FENs, the edit menu can still be useful if you just want to displace one or two pieces in an existing position. But you are correct about the inability to enter castling rights. I think I should definitely add this; I considered the edit-position menu important enough to also add the fairy pieces on that menu. It should be easy enough to add a menu item that endows the piece with castling rights. I will put this in for the next version.
I am not sure about move number and 50-move counter: in practice this will almost never be a problem. People that care about them can use a FEN. The eedit-position menu is mainly meant as a quick and dirty way to change a position. In principle it always interrupts any game that was in progress, so there will never be any moves known from before editing the position. This means that internally, WinBoard will always consider the move to be move number 1, printing the position in the PGN file before the first move.
Currently, to set up a specific FRC opening position, you would have to know its number. You can then type this number in the "new FRC game ..." menu popup dialox box. It will then continue to use this opening position until you select a new one. (Youi can also type -1, or click 'random', and then it takes a different random position all the time.) I still am considering adding a button in this dialog box where you could make the current board position equal to the new FRC opening (of it is a valid opening), and compute the number for you. I will have to overhaul this menu anyway, to implement CRC and the various 10x8 variants.
