Attached File

Will it have a CHOPPA on top

Because that's an AWESOME shooting position

Stack them...

First thoughts

Do Not cut through the walls of your conex, this will not make it water tight.  

If you are going to be shooting through windows: Make a wall about 7' out from the wall of your conex with the windows in that.  Skin it on one side with plywood.  Tie it back to the conex roof with rafters ever so often (24" on center if you want to make a real roof there, or whatever your local building code is).  No you can shoot from those positions and if someone launches a round through the wall you have not lost the structure of the conex.  This area would also be ADA accessible if that is a concern.

Later if you like you can put a roof from the wall to the conex.  This will give you an option for covered classroom, work space, etc.  My choice of 7' out from conex might not be ideal for you, I am thinking in terms of 1 sheet of plywood from the box to the wall (40' container then would be 10 sheets of ply).  You can go out as far as you want to or need to with rafters, just costs more.  

Top of box would make a great place to modify to shoot from; however, ADA access might be a headache if needed.   A roof there would be nice for rain, and shade protection.  Again this can be added later.  

Later thoughts

Do you have power at the range?  Is it nearby your placement area?  IIRC you have earth moving equipment.  If you dig a trench out there either run power and water lines or conduit for them in the future, also communication lines down to the main range area.  Will you need or want lighting out there?  If no power are latens enough?  Solar lights?

Have you considered safety protocols?
When shooting from the roof, noone is allowed in the conex.
When doing firearms maintenance in the conex no one is allowed on the roof.
How do you secure the entrance to the range when using the conex?  Can people make it between you and the berm easily?  Will you need to install a gate or signal system so no one ends up down range on a hot range.

All of this can be phased into place.

Last thought for now
Would a concrete block structure be better?  More expensive short term, but long term might be the best option.

TDSA has a CONEX tower.  View from the top:


Ft Wolters has a MOUT training area built out of CONEX's:

We've cut/framed quite a few openings in conexes (openings big and small, sometimes with stamped drawings sometimes without the need), and the results have to be watertight, it's a fairly simple thing that's done all day across the country.

If you intend to make larger openings that require reinforcement, I can send you examples of engineered solutions that are legit in seismic Zone 4 areas. It's really simple, cheap and easy to reach those levels (at least it was before biden ramped up steel prices) and could be considered overkill for most of the U.S. but you would have no doubt in your mind.
BUT, if you ever intend to move your conex, it will survive the forklift ride , or if the foundation erodes, etc, etc with the additional reinforcement at openings. small windows don't need much, the window framing can be enough.