Add onions and jalapeños to pan with hot oil; cook on med-high heat for 5 minutes until the onions just begin to brown. At that point, add the garlic[ cook for a minute.
Add the tomatillos to the pan and reduce heat to med. Cook for 10 mins or until the tomatillos are cooked through but still hold their shape. Slowly add salt to the tomatillos as they are cooking in the pan.
Add clam juice to the pan, and cook over high heat until the liquid has reduced to about half the original amount.
Add cheese and shrimp to the pan and cook for 10 mins in a preheated 425 oven.
Stir in cilantro, black pepper and lime juice before serving.