So I recently downloaded a mod for Fire Emblem Fates and when I booted on. It shows significant lag when I'm engaging a fight with an npc. Mines a 3DS XL model. Does anyone have a solution to have it run smoothly?

Um, 64kb is the max cluster size on FAT32, 128kb+ is nonsense.If you have a 128GB card, the allocate unit size when originally formatting your card as FAT32 should've been 64kb (Afaik it works for me great)
Depending on the card size & allocate unit choice, the speed for loading on your console will be the same like <= 32GB cards if set correctly
Btw, a list for cards bigger than 32GBs:
64GB = 32kb / 64kb
128GB = 64kb / 128kb
256GB = 128kb / 256kb
512GB = 256kb / 512kb
Though sizes > 128GBs isn't recommended as mentioned here ("What kind of SD card does my console use/need?")

I haven't double checked cluster sizes on FAT32, so my bad :')Um, 64kb is the max cluster size on FAT32, 128kb+ is nonsense.
The 32GB limit is an arbitrary one that Microsoft set back in the day when it still seemed like a lot and it was never changed because the format dialog wasn't updated in over 30 years. There's no issue with larger partitions, the 3DS just has that one particular bug.I haven't double checked cluster sizes on FAT32, so my bad :')
That must explain why > 128GB cards have issues then, since you can't go higher than 64KBs, and the allocation table needs more space to handle such big sizes to prevent corruption and I/O problems
(And also explains why Windows only allows up to 32GB cards to be formatted as FAT32, making sure it's better safe than sorry for potential future corruption)