After reading this I went ahead and did some research on the effects of exclusive items. I expected them to be hardcoded and basically impossible to edit, but turns out they are not! You can change the effects of exclusve items or add new ones with some hex editing.
Here's what I found out:
There is a table inside arm9.bin that goes from 0x98568 to 0x98CD9 which contains one entry for every exclusive item in the game, including the last 48 dummy items at the end of the list. Each entry has 2 bytes:
The first one is the ID of the effect the item has, which ranges from 0 to 0x80 (Both included, 0 means no effect)
The second one is used to address the stat buffs table (see below). 0 means the item does not buff any stats.
I guess you replaced some of the unused items, so to give them an effect you just need to go to the part of the table corresponding to the unused entries (It starts at 0x98c80, every entry is 00 00 from that point on) and change the values there for each item.
This is the list of effects: (I have checked only some of the random chances, but it seems that they are always the same for similar effects)
The stat buffs table starts at 0x9852C and ends at 0x98567, right before the effect table. It has 15 entries, each one is 4 bytes long.
Each of the 4 bytes indicates how much each stat is buffed by the item (Order: Atk, Def, SpAtk, SpDef)
For example, if an exclusive item has its second byte on the effect table set to 3, the buffs granted by it can be found at 0x9852C+4*3 = 0x98538 = [10, 0, 10, 0]. An item with this value would increase attack and special attack by 10.
So if you want an item to just give a stat boost you would need to set its first byte on the effect table to 0 and the second one to 1-14, depending on the stats you want to increase. Keep in mind that you can't change the values on the stat buffs table without affecting every other item which uses the same entry there.
Getting the items to show up in Croagunk's swap is going to be trickier though. If you look at the list you will see that all the items that follow the *, *, **, *** pattern are together between position 506 and 1013. The game only checks if you have the required items to create higher rarity ones within that range, that's why yours don't appear on the list.
Fixing that would require to write a rom hack that changed the behaviour of the code that does those checks and then create a patch to apply the changes on the rom.