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I still hope we can implement a solution that allows members to do this without any editorial help. It shouldn't be that difficult to have a 'custom' option in the piece-set selector of Game Courier, and a text entry where the user can specify the directory where he uploaded the images.

Fergus did add the ability to customize the graphics used, described here.  It's a little complicated, but I used it when making the preset for Royal Court rather than making a new piece set.

... I think the site would also benefit from a more organized presentation of the available piece sets.

This is definitely needed.  I have a spreadsheet I made to help me track some of some of the set groups.  You can download it here.  But something more comprehensive is in order.

Also, I would like to know how to group sets together...

Each piece set is defined in a php file.  The format of that file is described here.  The file /play/pbm/sets.php contains the list of all piece sets, and to which group they belong (if any, otherwise defaults to "unique").  The ability to put multiple piece sets into a group is an important feature, allowing each player to choose which set to use.  (e.g., I can use abstract style pieces even if my opponent wants more standard-looking pieces.)