I have cloned all the ones that can be cloned. The others cannot be cloned because of their own limitations
This is untrue. You have cloned every "item" in the list of data.raw.item. But not every item is actually contained in that list. Rail, for example, is actually located under data.raw["rail-planner"]; firearm magazines and other bullets are under data.raw.ammo, modules are under data.raw.module, etc. There are several item types that you could be cloning, but you aren't.
I know this, because I have a similar for loop in one of my own mods, Reverse Factory, which has to go through every item in the game, and create a reverse recipe for it, so that it can be recycled in the machine.
As evidence, an improved version of your mod here. You can test it out for yourself, but I made it work with all of the item types listed below:
--List of item types, excluding armor (generally non-stackable) and fluid
local itemTypes = {
"ammo", "item", "rail-planner", "gun", "capsule", "module", "tool", "repair-tool", "item-with-entity-data"
}
The actual for loops I used:
for _, itemType in pairs(itemTypes) do
for _, item in pairs(data.raw[itemType]) do
...