You're right. Up till the time Western uniforms were used in the Boshin war,
there wasn't anything even remotely close to a uniform for Choshu. Up till
the time Satsuma joined in, the Choshu people operating in Kyoto were
essentially operating independently, so they were very cash-strapped (like
Shinsengumi), and thus were likely to wear just their average street
clothes-- kimono, hakama, and the like. Outside of the realm of Western
uniforms, the only thing remotely close to a uniform with traditional
Japanese clothes would be a haori with the crest of Mori (lord of Choshu) on
it, which looked like this:
http://www.samurai-archives.com/kamon/mori.jpg
But even then, wearing the lord's crest would only really be allowed to
high-ranked samurai, I believe.
Let me know if there's anything you need clarified.
-M.