These references do not appear in the .ll file. They are injected when the .ll file is compiled to object files.
I think something in your code triggers a reference to one of the other injected functions and that pulls in the CRT.
Try compiling your test file into an .o or .obj, that is, without linking. Then dump the symbols in the object file to see what symbols are referenced. I suspect you'll see other references to symbols in CRT and you will have to replace those as well with stubs.
Unfortunately, I don't remember the linker flags to replace/suppress the default CRT libs. Well, actually, you might compile to .o / .obj and then manually link on your system. If you're using MSVC check the options to its "link" executable (I don't remember the exact name of the MSVC linker).