capstone==3.0.5 still tries to build for both i386 and x86_64, this is already fixed on master and will be released with the next version. Looking at the Makefile, there are two possibilities:

1. Turn off MACOS_UNIVERSAL:

   $ MACOS_UNIVERSAL=no pip install capstone
   

2. Install the development version from current master branch, with LIBARCHS already adapted for Mojave:

    $ pip install "git+https://github.com/aquynh/capstone.git#egg=capstone&subdirectory=bindings/python"

Make sure you use quotes in the last command or escape the ampersand (&), otherwise bash will cut the command and run in background instead.

Once capstone is installed, you will have to deal with unicorn in the same manner and finally should be able to install pwntools. I didn't test it anymore, but the one-liner for the installation will be

$ MACOS_UNIVERSAL=no pip install pwntools

According to the author @eli-bendersky, pyelftools is a module for parsing and analyzing ELF/DWARF files and it has no direct way of modifying them. I had a look at the module source files and could not find any methods to edit/save either.

On the introductory post, within comments author acknowledges that pyelftools has no API-level support to do this but some tinkering around can help achieve what you need.

If pyelftools is not a hard dependency, here's an example on how to do the same using elffile:

Copyimport elffile

eo = elffile.open(name="/bin/ls")
eo.fileHeader.shnum = 30
with open('./ls.bin', 'wb') as f: f.write(eo.pack())

Using readelf, you can verify that changes were saved correctly:

Copyreadelf -h ls.bin 
ELF Header:
  Magic:   7f 45 4c 46 01 01 01 00 00 00 00 00 00 00 00 00 
  Class:                             ELF32
  Data:                              2's complement, little endian
  Version:                           1 (current)
  OS/ABI:                            UNIX - System V
  ABI Version:                       0
  Type:                              EXEC (Executable file)
  Machine:                           Intel 80386
  Version:                           0x1
  Entry point address:               0x804be34
  Start of program headers:          105068 (bytes into file)
  Start of section headers:          103948 (bytes into file)
  Flags:                             0x0
  Size of this header:               52 (bytes)
  Size of program headers:           32 (bytes)
  Number of program headers:         9
  Size of section headers:           40 (bytes)
  Number of section headers:         30
  Section header string table index: 27
readelf: Error: Unable to read in 0x708 bytes of section headers

There's not much documentation on elffile but you can have a look at the source and figure out ways to replicate pyelftools-specific functionality. If that doesn't work, you can try using both pyelftools for reading/analyzing tasks and elffile to edit sections and write changes.