Katherine, see the second post, where I supplied many of the missing bits in the first post, including most that you've mentioned.

The men sang "Bryn Calfaria" as they were walking to the mine toward the end of the film (1.27:10). "Llef" was one of the hymns sung in church (1.41:40); I now notice it was also used during the death of Ivor (1.20:17). And you're right: the song as Pa and Huw were coming up from the mine with the body is "Penparc".

This fills in two more gaps in my chart:
1.20:17 Penparc: death of Ivor
1.56:xx Llef: ascent from the mine with the body

There remain only two bits unidentified: the dirge-like hymn as the men are descending into the mine and music behind the final credits.

Do you have words for "Peter O'Pea" (beyond the verse used in the film)?