How to embed fonts into PDF

Ghostscript can do that. One condition though: the font(s) referenced by the original PDF need to be present on the system where you run Ghostscript.

Here is an example command to run on Windows:

gswin32c.exe ^
  -sFONTPATH=c:/windows/fonts;d:/some/dir/with/more/fonts ^ 
  -dCompatibilityLevel=1.4 ^
  -dPDFSETTINGS=/prepress ^
  -dCompressFonts=true ^
  -dSubsetFonts=true ^
  -dNOPAUSE ^
  -dBATCH ^
  -sDEVICE=pdfwrite ^
  -sOutputFile=output.pdf ^
  -c ".setpdfwrite <</NeverEmbed [ ]>> setdistillerparams" ^
  -f input.pdf

The resulting output.pdf should have all fonts embedded which input.pdf didn't have. Just make sure that -sFONTPATH=... contains (at least) one directory where the missing fonts are found by the gswin32c command.