Whisk together the eggs, milk, salt, pepper, and flour. Eventually a thick, somewhat pasty batter will form.
Set it aside for about 30 minutes to rest and let the bumps even out.
In a large pan caramelize the two onions.
Bring a large pot of water to boil. Add plenty of salt to the water.
Reduce to a simmer.
Add cheeses to the large pan with the onions.
Push the batter through the dull side of a flat cheese grater with the back of a ladle into the simmering water.
Once the squiggly pasta is cooked (it should only take a couple of minutes – they’ll float when ready), add it to the pan of caramelized onion with all the cheeses.