そのページのこの辺は読んで必要そうなフォントパッケージは全部インストールしてあるの？

3.5. My favourite font has gone! The font Emacs uses is just boxes

Only minimal fonts will be installed after the upgrade from X.Org R6.8 to modular X.Org.

Font packages are now named font-<author/class>-<fonttype>

Some packages dependencies have not yet been updated for the fonts they require,
so you may need to manually install the needed fonts. For example, to provide the font
emacs wants to use by default you will probably want to install font-adobe-dpi75
(or font-adobe-dpi100 if you like large fonts). This package provides the courier,
helvetica, new century schoolbook and times font families.

The lucida font family is provided by the package font-bh-dpi75 (or font-bh-dpi100).
The monospaced version, lucida typewriter is provided by the package
font-bh-lucidatypewriter-dpi75 (or font-bh-lucidatypewriter-dpi100).

Note that after installing fonts you will need to restart the X server or run xset fp default;
xset fp rehash to make the new fonts available