Configuration shown in figure "E" could be a real problem, especially if there are operators on the side of the "blob" facing the door and someone is trying to enter or exit the room.  Consequently, this option has been eliminated.

Below are some sketches of the two levels and the "around the room helix".  The benchwork is 1 1/2 ft wide in the room and closet [this makes a 3 ft aisle in the closet which is barley enough, or maybe not enough].  There are three eight inch wide shelves in the storage room, one above another, which feed the top level, the bottom level and the helix [this provides various interchanges].  The number of operators would be 4-5. 

The "crude" software for the diagram is sufficient to scale out space.  Templates have been generated for curves, parallel tracks and switches.  Minimum radius is 24 " and the switches are scaled out to 12" which is just barely adequate for a number 6 switch providing a 2 inch space between parallel tracks.

The top level has a 56" inch "nod under" at the door and the bottom level has a drop track, or a swing track, crossing the door [in operation the drop/swing track would be used VERY little and the normal position is to have it out of the way].  The light gray 3/4 circle on the bottom level was a thought about a single turn helix going to a staging area under the yard or a single turn helix along the 13 1/2 ' wall but with the 24 " min radius, it doesn't seem like a good idea.

Yard location - it needs to be on either the top or bottom, not within the helix, with the bottom level being a preferred level.  That said, to maximize the distance between the bottom and top levels, it needs to be on either side of the door to give the greatest possible length of run to get to the 56" inch "nod under" at the door.  There is more wall to the left of the door than to the right so it was located to the left.  Should it all be against the 10 1/2' wall or curved around onto the 14 1/2' wall with at least a foot of straight beyond the curve before reaching the fowling point of the yard switches?  The way it is drawn, there could be some industrial area immediately to the left of the door and the line crossing the door on the drop track would come in behind the industrial area to feed the yard with a couple of interchange trains.

Estimated length of helix is 52 ft and an average grade of 2 1/2 percent gives an elevation of about 15.6 inches.