Your story might be buried under stacks of other manuscripts, or it could even have been lost. If you don't hear from a publishing house within three months, I think it's legitimate to call and pleasantly ask about the status of your work. I've built some very receptive relationships with publishing assistants through phone contact. It's good to have an assistant editor's ear. Editorial assistants aren't quite so busy and one day they may become editors.
Cover letters are a real art form.
They should be a brief brag, capturing attention without being obnoxious. You don't need illustrations to accompany a submission, and editors don't want to read your illustration suggestions. Doing either of these things may mark you as an unprofessional novice. Establish a habit of having envelopes ready and waiting to go to the next publisher. It's incredibly disheartening to have a manuscript returned, but as soon as it's back in the mail, you can hope again.