Ah you figured out the materials quest while I was writing a reply for it lol. Anyways, the church quest doesn't have an ending yet. I added a note at the end of the Goddess event that lets players know her limbs aren't actually available yet, but you might not have the version that has that message patched in. Basically, getting her limbs is the main quest for the rest of the dungeon, so they'll be spread throughout the rest of the dungeon but easy to find.
And I'll just copy and paste this again for the ghost mode thing since I just posted it below.
"In the church there are a number of secret entrances where it looks like a wall but you can walk through it. All of the intended instances of this will have some sort of hint indicating it. Mostly, it's little glowing footprints on the ground that seem to lead straight into a wall. Ghost mode is not intended and is caused by some sort of bug. The debug menu option "Fix phasing through walls" will correct this. If you remember where you encountered this specific bug, let me know and I can try and fix it. Thanks."