Here in Alma 13:4 Joseph Smith emended a present participial clause that in the earliest text is never completed by a main clause—namely, by changing the present participial having to the finite verb form have. It is possible here that the earliest reading, they having, is an error that entered the text because of the preceding they having at the beginning of verse 3 (“therefore they having chosen good”). On the other hand, as discussed under Enos 1:3, the original text has cases of stranded present participial clauses. For that reason, the critical text will restore this instance of they having here in Alma 13:4.
David Calabro also points out (personal communication) that present participial clauses are also found throughout subsequent verses in the larger passage, with only an occasional main clause; and in a couple more instances (marked below with arrows), the present participial clause is introduced by thus (just as in verse 4, “and thus they having been called”):
Thus the original text in Alma 13:4 is consistent with usage elsewhere in the larger passage.
Summary: Restore the original stranded present participial clause at the beginning of Alma 13:4 (“and thus they having been called to this holy calling”); such disconnected usage is found elsewhere in the earliest text.