for subtitles they used to use Sub Station Alpha (i think they still use it) its great for customising subs and for
karaoke mode. Its also good for timing since you can import a wav file into it but Virtualdub could also be used for
timing but its hard without the sound. For timing I use Subtitle Workshop cause you can have the movie playing at the
same time.
Encoding would be VirtualDubMod or some kinda of varient.
Translating proberbly notepad hehehe.
Other stuff like quality check would rely on your knowledge of Japanese and a keen eye for watching subtitles.