The 1830 typesetter added the perfect auxiliary had, but there is no need to put the verb phrase in the past perfect. Elsewhere in the text there are instances where the verb phrase in an after-clause does not take the perfect auxiliary have:
Thus the original reading in 1 Nephi 19:3, without the perfective had, is quite acceptable.
It may be that the 1830 typesetter simply expected the perfect auxiliary. Usually in the Book of Mormon, the verb of the subordinate clause is in the past perfect when the following main clause is in the simple past tense. For instance, when the initial subordinate clause begins with “after (that) I”, the finite verb is typically the past perfect had (21 times). But such a tendency does not mean that the perfect auxiliary must be there.
Summary: Remove the intrusive had that the 1830 typesetter added when copying the subordinate clause at the beginning of 1 Nephi 19:3; although the had is expected, there are other examples in the text without the had.