Maybe you could so something like my Ford Ranger has. It has a floor "storage place". It doesn't run all the way up to the seat. Mine doesn't have a cup holder, but I have attached a picture of one that does.
http://73-87.com/7387garage/interior/console.htm
That link is to a fantastic article on building a custom console in a square body. Obviously he is using bucket seats, but it could get you started.
For a cup holder, The only idea that comes to mind is cut a hole, and use a drop-in cup holder similar to the one used in motorhome dinette
tables.