The fonts can be installed via the bash shell from cygwin. Also you need to make sure that the right packages in cygwin are installed. A mininal setup and the texlive-font-fontutils (which contains the LCDF typetools) should suffice. (Alternatively the source source code of LCDF Typetools may be used.) Then, for building the files you can follow the description on github. The binaries of the LCDF Typetools for Windows are not required with cygwin.
Building
1) Put the sources in a FOLDER:
2) Copy your OpenType font files for MinionPro into the otf directory.
$ mkdir $FOLDER/otf
$ cp /some/path/*.otf otf
3) Run ./scripts/makeall for Minion.
$ ./scripts/makeall MinionPro
Now repeat steps 1-3 with a new folder, but replace MinionPro with MyriadPro. Alternatively you can use the same folder, but then you have install the font first and run $ ./scripts/clean before starting with Myriad.
Installing
Installing is only a bit different from the description on github.
Run ./scripts/install /cydrive/c/path/to/Miktex in the cygwin bash. Note that c/path/to/Miktex has to be replaced with path to the local Miktex installation, but cygdrive is the folder where the windows drives can be accessed. (A local texmf tree can be created in MiKTeX for this purpose. Instructions found here. Then we may run something like ./scripts/install /cydrive/c/localtexmf in the Cygwin bash.)
In the windows prompt run initexmf -u
In the windows prompt use the command initexmf --admin --edit-config-file updmap. Then add
Map MinionPro.map
Map MyriadPro.map
and save.
In the windows prompt run initexmf --mkmaps
Now everything should work and you should be able to use the fonts via \usepackage{MinionPro} or \usepackage{MyriadPro}.