Regarding pomegranates, I have counted many a pomegranate, and I’ve never gotten one with 613 seeds. However there are several sources that say that there are 613 seeds:
Derashos Chasam Sofer volume 2 ??? ????? ???”?:
????”? ?????? ?? ????? ?? ?? ???”? ??????’ ??? ???”? ????
Malbim Shir Hashirim 4:3:
???? ???? ????? ???? ??? ???”? ???????
Lachmei Todah ????? ?”? ???? ???”?:
?????? ?”? ????? ????? ????? ????? ???”? ?????? ????? ???”? ????
Eitz Yosef Shir Hashirim Rabbah 4:3:
???? ???? ???? ???? ???? ??? ????? ?????? ??? ???? ?????? ?? ???”? ??????? ??? ???”? ?????
Niflaos Hatiferes Shlomo Ose 225:
????? ??? ????? ??????? ?? ?? ???”? ???????
Yosef Be’ohr Al Megillas Shir Hashirim 4:3:
???????? ????? ?? ???? ?????? ?????? ?????? ???”? ??????’ ????”? ???? ??? ???? ??? ???? ???? ???? ??? ?????? ?? ???
All these sources are from the past couple of hundred years. I have yet to find any earlier source. Which is interesting because none of these sources are quoting each other (except for perhaps the last one) so it seems as if there was some sort of earlier source or tradition.
Regarding the Chofetz Chaim, there is a version of the story in the biography written by his son. I will hopefully post the quote later.