Thanks for starting this thread - I've been looking for a place to discuss / ask questions on this one too.
I also started running this AP in January. My PCs just hit level 2 last session, so they still have 3 main quests to do in Chapter 1.
For your specific topics:
-Relics: I agree that it's going to be a little tricky from a narrative perspective for non-dwarf PCs to be given these relics, and I'm also worried about that (my PCs are ALL non-dwarves). I think many of the campaign backgrounds from the Player's Guide give good reasoning for why the PCs would be very interested in Dwarven culture though.
-Relics pt2: In terms of moving things around, I've considered moving Kalmaug's Journal (from Cult of the Cave Worm) to Chapter 2 of Mantle of Gold. Not sure if I'll actually go through with that, but it could be a good/useful option for a prepared spellcaster PC.
-Ygrin/Tuom: I really like your idea for Ygrin releasing the protean, I might borrow that as well!
Other thoughts I've had so far:
-In the Blacknoon Gauntlet, I adjusted the treasure on the dead thief that had a shadow rune (seemed incorrect without having armor potency, as discussed in a different thread here). I replaced the armor rune with Charlatan's Gloves.
-Speaking of underutilized characters, I'm trying to figure out how to introduce Narseigus and Queen Frilogarma earlier. For Narseigus, I may try to incorporate him in Guldrege in some way (perhaps he visited Workshop Heights looking for more about the worm and Thenur remembers him?). For Queen Frilogarma, I'm planning to use her as an important character for the party's witch PC (i.e., I'm going to connect the Queen to the witch's patron).