I don't think that you can mix and match between the body parts and the battery trays/boxes for NA1 & NA2.
If using the NA1 body part, you have to use parts 21, 26, 27, 28, 29, 30 & 33 from the left side of your original parts diagram.
I can't see that the NA1-R uses a different body piece - the part number is the same.
The NA1-R battery is a different physical size to both the Type S battery and the standard NA1 cars, as far as I can see from the Amayama parts diagrams that I am looking at.
i don't think that the Type S battery is compatible with the NA1 ladder body part, as it wasn't designed to be.
Your choice, is to go for NA1-R battery, or the battery for the standard NA1 - there isn't factory hardware to secure the NA2 S battery to the NA1 ladder body part, as far as I can see.
The factory S-Zero uses 60500-SL0-J00 instead of 60500-SL0-030 which is the body part on my Type S.
The S-Zero uses a physically smaller battery too, which leads me to deduce that the J00 part is smaller than the 030 part.
The S-Zero battery is the same as the NA1-R battery, and uses part
#30 , but not
#28 to attach to the different (later) ladder.
In other words you can't put an NA2 battery on the NA1 ladder body part, unless it is the S-Zero battery (AKA the NA1-R battery).
CAVEAT - All the above is for RHD cars - your LHD NA1 ladder appears to be the mirror image of the RHD equivalent, but I can't tell from the diagrams if the slots and holes are compatible... they do have different part numbers.