manual intermediate shaft - I don't think it matters, but an intermediate shaft connects the CV axle to the tranny
rear tranny bracket-Depends on what kind of car. Since this is in the HONDA tech section, I'll take it that you're asking about hondas. Well there's a Tranny mount but not a rear tranny bracket. There is a rear motor mount.
clutch master cylinder - this is for a Hydrolic Clutch System on most hondas. This is used to pump fluid that eventually disengages the clutch.