I finished the second dungeon, and when I picked up the conch I got stuck in an animation loop? Anyone else have a problem like this?

Yeah, I got the same issue!

I tried doing this and it didn't work for me

Couldn't get past first temple - Link's Awakening DX HD community - itch.io

It looks like I fixed it by messing with my save file. I backed it up somewhere first, and then added this line to the end of the current save file:

s d2_instrument 1

I thought this meant something along the lines of "Link has the instrument from the second dungeon," but this didn't actually make it work. After reverting the save to my backup, I picked up the instrument again and it seemed to work fine, I don't know why.

exactly the same solved for me, when I re-enter the game with s d2_instrument 1 set, the instrument was not there, I exit the game, reverted the file (deleted the line manually) and then it workd.... weird, thanks GoldenStein64