Cook the pasta shells according to the package directions. Drain well, rinse under cold running water and drain again.
Invert the shells onto paper towels to cool while preparing the filling.
In a large bowl, whisk one of the eggs until just slightly foamy. Add the crabmeat, cheese, scallions, tomatoes, basil, thyme, salt and pepper; mix well.
Use a spoon to stuff the shells with the crab mixture, dividing it evenly among them.
In a small bowl, beat the remaining egg with the water. Place the bread crumbs in a shallow dish. Dip each shell into the egg mixture shaking off any excess, then roll in the bread crumbs.
In a large, heavy saucepan over medium-high heat, bring about 2 inches oil to 365 degrees.
To help maintain the oil temperature, add the shells a few at a time without crowding. Cook about 2 minutes or until golden brown. Remove with a slotted spoon and drain well on paper towels. Repeat until all the shells are fried. Serve warm.