I would suggest starting shelves off the floor as to allow you to store larger items "under" the shelves like cases of water, etc. I would also suggest maybe talking to a custom trim/woodworking person about giving you an estimate since your space is unique.

Does the door to the room swing in or swing out? Especially if it swings out you have the opportunity to do shallow shelves on the wall to the left of the door, which is great for things like soup cans and other single objects. If the door swings out it could be as deep as 8", if it swings in you would probably be limited to 6" and have to install a door stop, plus you would need to close the door to access the shelving. Definitely not ideal, but still extra storage space it would be a shame to give up. Note that I don't believe Elfa has any systems that could fill such a shallow space.

I would also definitely consider running the last shelf under the lowest part of the stair along the back wall instead. That looks like it will get you an additional 12" or so of shelves that will be easier to get to and view as you will be able to stand in an area of higher ceiling height rather than have to crouch down to see what's in that last shelving unit.

I think I would orient shelf 1 (the shortest shelves) perpendicular to the other shelves and make it 18 to 20 inches deep and store paper towels, paper napkins, plates etc... extra foil and plastic wraps.

Could store large unused appliances, juice pitchers there also.

Also, be sure to add good lighting that comes automatically on whenever you open the door and turns off when you close the door.

Given the narrow width of the pantry at only 39.75", have you considered doing shallower shelves? 8"-10"? Most items would fit on there (I suggest measuring a few standard items that you will store in the pantry, e.g. cereal boxes, flour bags, etc.)

You could make your shelves L-shaped and have a deeper section 15"-18" along the short wall (39.75").

Are you doing anything on the left side? Looks like you would have full ceiling height there and so it might make sense to plan for storage on that side as well.

Id make this 2 closets or maybe even 1 and “waste” space. I would cut off the long tail of the L and have a shallower wide pantry. Basicallg that’s extending wall 3 all the way to the right. This may even be a reach in rather than a walk in

you could then use the top part for different storage, maybe a small closet accessed from another room. Or there are creative under stair options like drawers.

Just my opinion. I’d rather have things closer.

May we see pictures of the space -- exterior area around the pantry and a shot in the open door so we understand what you are working with?

Make sure you have plenty of light shining on all shelves - you need to be able to see what you're reaching for.