In both these verses, the original text read “had came”. The dialectal use of the simple past-tense form came as the past participle is an important characteristic of the original text. In the first example (in verse 1), came was edited to the standard come in the 1849 LDS edition and the 1874 RLDS edition. In order to deal with the second example (in verse 4), the 1849 edition deleted the perfect auxiliary had, but the corrected 1852 edition (the second printing) restored the original “had came” (probably by reference to the 1840 edition). This second “had came” was edited to the standard “had come” in the 1874 RLDS edition, while the LDS text has conformed to the standard since the 1907 vest-pocket edition. See the discussion in volume 3 under past participle.
It is also possible that in verse 4 the deletion of the perfect auxiliary had in the 1849 LDS edition was accidental, especially since the phrase “it came to pass” is much more frequent in the Book of Mormon text than “it had came/come to pass” (of which there are only two other occurrences in the text, in Helaman 6:18 and 3 Nephi 1:20). For another possible example of the tendency to delete the perfect auxiliary in “had came”, see the discussion under Helaman 16:1.
Summary: As already noted, we follow the earliest textual sources in determining the form of the past participle; here the original text in 1 Nephi 5:1 and 1 Nephi 5:4 read “had came”.