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I figured it out after several hours of headache! Here is the solution:
/give @p minecraft:black_shulker_box 1 0 {BlockEntityTag:{Items:[{id:black_shulker_box,Slot:0,Count:64,tag:{BlockEntityTag:{Items:[{id:stone,Slot:0,Count:64},{id:splash_potion,tag:{Potion:"minecraft:water",CustomPotionColor:16777215,CustomPotionEffects: [{Id: 2,Amplifier: 100,Duration: 199999980}, {Id: 14,Amplifier: 1,Duration: 1999980}],display: {Name: "Glitch"}},Slot:1,Count:64},{id:stone,Slot:2,Count:64},{id:stone,Slot:3,Count:64},{id:stone,Slot:4,Count:64},{id:stone,Slot:5,Count:64},{id:stone,Slot:6,Count:64},{id:stone,Slot:7,Count:64},{id:stone,Slot:8,Count:64},{id:stone,Slot:9,Count:64},{id:stone,Slot:10,Count:64},{id:stone,Slot:11,Count:64},{id:stone,Slot:12,Count:64},{id:stone,Slot:13,Count:64},{id:stone,Slot:14,Count:64},{id:stone,Slot:15,Count:64},{id:stone,Slot:16,Count:64},{id:stone,Slot:17,Count:64},{id:stone,Slot:18,Count:64},{id:stone,Slot:19,Count:64},{id:stone,Slot:20,Count:64},{id:stone,Slot:21,Count:64},{id:stone,Slot:22,Count:64},{id:stone,Slot:23,Count:64},{id:stone,Slot:24,Count:64},{id:stone,Slot:25,Count:64},{id:stone,Slot:26,Count:64}]}}}
I wanted to change the color id of a potion from pink to black or white and I put this in after the tag: bracket {Potion:"minecraft:water",CustomPotionColor:16777215, and it came out how I wanted it.