I have StackSizeController installed and all of my items stack as intended, but when I try to add a stack of equipped items to the kit it only equips one of each and puts the rest of the stack in my inventory. Is there some code I can edit to fix this? 

If you pick up a wearable item you cannot place it on top of an existing (same) item in the clothing slots. you have to place it in your inventory first and then move it over. I assume that the plugin will see the slot is occupied so moves it to inventory.