You want `emb` to be `yes` for all fonts (and possibly `sub` as well; also, all fonts should be Type 1, not Type 3). By default in Ubuntu, pdflatex should embed all fonts. Just in case, you can check `/etc/texmf/updmap.d/00updmap.cfg`, which should have a line like this:
If it's set to `false`, change it to `true`, then run `update-updmap` as root. Remake the PDF; if it still has non-embedded fonts, your figures are probably to blame. Check your PDF figures and make sure their fonts are embedded (using the `pdffonts` command). For anything that doesn't have embedded fonts, you can try the following magical invocation:
This creates a file `figures/Mprime-new.pdf` that is hopefully identical to the input file `figures/Mprime.pdf`, except that the fonts are embedded. Run `pdffonts` on it to check.
Once all your figures are in PDF format, remake the paper again. Hopefully, all your fonts are now embedded --- check again with `pdffonts`.