I didn't think stop bath had much of a smell. Sure it's not the fixer making the big fume? Fresh fixer can take your breath away if you stick your nose down in it. If the stop bath bothers you, mix it half as strong. Plain water doesn't do much, and makes your fixer die an early death.
Time I spent in the darkroom in the late 1970's is why I can't stand the smell of vinegar, even now. Ammonium Thiosulfate, the main ingredient in most rapid fixers, is not naturally acidic, fixers are only acidic, because they add (typically acetic) acid to them, to make them acidic. This was done in the early days, because hardeners needed acidic fixers in order to work. Few films need hardening fixers these days, and recent developments have discovered, that fixers don't need to be acidic. Now I don't know about bleaches, whether they need to be acidic or not.