I Farmed Daiku cave for awhile and didn't get anything. I heard that the House of Hinawa was a good place to farm. Two runs in I got one of the the five i need for the severance and isolation quest, so i popped a 200% drop booster and farmed it for a full hour without getting another. It's incredibly disheartening to know i have spent maybe two roughly two hours in total farming to only get one of the five I need. Is there any other farming spots that are better or any other methods of obtaining these marbles?

You're on the right track with daiku cave and house of haniwa (from treasure chests), but as you say, the drop rate is very finicky. For the purpose of main story quest completion, there are other ways to get it:

1. Doing sub quests.
-Popular Potato; collect sticky yams.
-Clear Kaguya's Home; kills a certain number of monsters.

2. Trade Kaguya with Zenith Medals.
-Complete Oni difficulty dungeons(not wardings); you can party to complete these. 3 runs per dungeon daily, so it may take a day or two(or three) depending on which dungeons you run. Satan and Hades are relatively straight forward. Past events had also given these out freely with login calendars or items trade nyankoropon. Check if you might already have enough in inventory for 1 or 2.