1.) One way to create a VAL file is with the spreadsheet designer built into NPM. This is shown in the "Specify the Design" section of the documentation
  http://people.cas.sc.edu/rorden/mricron/stats.html
2.) While the graphical editor is easy to use, these are simple text files, so you can edit a VAL file with your favorite text editor or generate them with your favorite scripting program.
3.) As noted whenever you run NPM, the NPM program is deprecated. While I hope it is robust and useful, active development has shifted to NiiStat that has a lot of new features. With NiiStat you design your experiment with an Excel spreadsheet:
  https://www.nitrc.org/plugins/mwiki/index.php/niistat:MainPage