It might have been better to keep the food in a nylon stocking, or to use grocery store shrimp. That beeing said, You did not Destroy your tank. DO NOT do a 100% water change or change the filter cartidges. You did the right thing fishless cycling the tank, but no rotting food is not good in the tank. It was rotting, and it caused enough bio lode to equal fish poo and create ammonia. now that you are going to add fish that will create the ammonia, you need to get the other stuff out.
A bottom feeder wont clean the tank, anything it eats comes out the other end.
If the gravel is that dirty, scoop it out rinse it several times in hot water, put back only enough to cover the bottom and hold down some plants. the leass gravel you have, the easier it is to keep a clean aquarium.