There is a lot of evidence out there that James used a Mark IV on the Black Album. First of all, if you watch the video "A Year and a Half In the Life Of..." you can see it all over the place. Also, there is a "Classic Albums" dvd about the Black Album in which they talk about some of the gear that was used. You can hear an early demo version of Enter Sandman, which Hetfield claims "must have been the Mark IV." To what extent it was used is not quite sure, but it was certainly in his arsenal at the time "Metallica" was recorded.
Kirk has claimed quite extensively that he used a combination of different amps including Mesa's, Marshall's, etc..., to achieve his lead tones on that album.