Suggestion 1: Especially if you are serious when you say that this part of the layout will be five feet off the ground, cut the width of this yard down to 2 feet thick, MAXIMUM, and only 1 foot thick behind the sump pump. This will prevent you from having to build a difficult to build and difficult to maintain 3x3 foot removable sump pump access hole, and also allow you to actually see and reach the track.
Suggestion 2: With your nice long mainline running the whole length of the room (what, 17 feet?) you have enough space for about 12 feet of yard. A foot-wide yard gives you room for four tracks, so you build a double ladder, starting with the mainline running along the back edge TOWARDS THE FRONT. This means all the switches on the ladder tracks will be accessible without having to reach over the yard itself--easier to see how switches are facing, etcetera. You'll have room in unused corners for a RIP track and caboose track.
It will be a lot simpler than what you have posted here. To give you an idea of capacity, my own layout's yard is half of exactly this space--12 inches deep, six inches wide--with a single ladder, four tracks deep, with a RIP track sticking out at the end of the ladder. My yard can hold around 24 40' cars without blocking the mainline. Yours should be able to hold 48 40' cars--or, figure, more like 30 or 40 60'-80' modern cars.
Suggestion 3: For the right-hand side of the area described, you have two feet of depth to work with. The main yard is using the back 12 inches, so put your single-ended intermodal ard in the 12 inches closest to the layout edge. 2 or 3 tracks, running around six or seven feet each, should be room for plenty of intermodal cars.
Bottom line: Look at real yards--they tend to have VERY LONG TRACKS. By making your yard skinnier with longer individual tracks, you maintain a high capacity, use fewer switches (reducing cost, complexity, wiring and derailment problems) and can easily reach the whole area. If you have to get at a sump pump or something often enough to need a lift-out in such a complex area, you're better off not covering it at all.
Something like this: