I'll probably add to this list as I go, but these are the stacked items I've noticed so far:

All 4 Angels Fish [alien-fish-1-raw] and 2 and 3
Dormant Quillnoa Seed [temperate-4-seed-dormant]

Looking at items.lua, I see the fish there, but there is a typo for the seed. You put 5 instead of 4.
I edited that 5 to a 4, and the seed shows up now.
But I have no idea why the fish don't show up - they are correctly named, from what I can see.

Okay, fixed. I have no idea what I am doing, but these are the changes that got the items to show up. (Hopefully I didn't break anything)

Line 543:
Change "temperate-5-seed-dormant",
to "temperate-4-seed-dormant",

Line 828:
I copied what you did with:
if Items.items["raw-fish"] then
Items.items["raw-fish"].type = "capsule"
end

and added these if statements:
if Items.items["alien-fish-1-raw"] then
Items.items["alien-fish-1-raw"].type = "capsule"
end

if Items.items["alien-fish-2-raw"] then
Items.items["alien-fish-2-raw"].type = "capsule"
end

if Items.items["alien-fish-3-raw"] then
Items.items["alien-fish-3-raw"].type = "capsule"
end