There are two minor editing changes in the clause “but it all were vain”. The lack of agreement between it and were was emended in the 1920 LDS edition by replacing the plural were with the singular was (giving “but it all was vain”). In the 1953 RLDS edition, the editing was extended. Not only was the number of the verb adjusted, but the word order was changed and the preposition in was inserted before vain (giving “but it was all in vain”).
Of course, the subject it all can be interpreted as referring to the entire process of trying to convert the Lamanites, but the use of the plural were suggests that it all can also refer to the preceding many means, a plural noun phrase. Given this latter interpretation, the plural were is acceptable. For another example of a singular subject form taking a plural verb (given that the subject is semantically plural), see the discussion regarding “the fruit were equal” in Jacob 5:74.
The reading of the current RLDS text (“but it was all in vain”) seems to follow the colloquial style of today’s English. In the Book of Mormon text there is some competition between vain and in vain in the expression “to be (in) vain”, but “to be vain” dominates:
vain (10 times)
in vain (5 times)
Notice that the last example (in Mormon 5:6) has the same phraseology that the current RLDS text has for Jacob 7:24 (“but it was all in vain”).
In any event, the text permits either “to be vain” or “to be in vain”, so in each instance we let the earliest textual sources determine the reading. In addition, the text has one other example of it all:
So there is nothing inappropriate about it all. Thus here in Jacob 7:24 we maintain the original reading, without the in and with the original word order (all were).
Summary: Maintain in Jacob 7:24 the original reading “but it all were vain”; the use of the plural were with the singular it, as well as the word order all were, appears to be intended.