Latin Modern works fine with Japanese.
If "lmodern" is set for \font_roman the "lmodern.sty" package sets
sans-serif and teletype to Latin Modern fonts as well.
Therefore, \font_sans and \font_teletype are better left as "default"
(less preamble code) in the LaTeX source).
Re-structure and rename files in a transparent way. Most template/example
names now correspond to the (verbose GUI) name of their layouts.
Note that this, most prominently, also changes [LANG/]splash.lyx to
something less insiderish, namely "Welcome.lyx".