Sorry, I was trying to catch up on things and completely forgot to write on the other stuff.
Cover Letters: Well, these are pretty standard. Keep it simple. List that it is a manuscript for their viewing. List your other publish works (if you have any). Don't write exactly what it is about but list what it is (mystery, sci-fi, social fiction, etc.).
Other letters: If you have not heard from a publisher, send them a friendly reminder message and give them a deadline (say about one or two months.) Remind them that if they do not read it, that you will submit your work to another publisher. Afterwards, if you still don't hear from them, then write another one stating that you will be taking back your work to be submitted somewhere else. If it is a short story, you can reduce the time frame (about one week, I think)
Publishers: If your novel is going to be published or plan to, think of the following: The printers have a certain of slots for each publisher. Those publishers divide the slots into categories. Usually, the big time authors get precedence over small time or new up and coming authors. Plus, if the missed the deadline, you have to go back on the waiting list. If the big time authors miss their deadline, they can potentially bump you as well.
Contracts: Things to consider in contracts. The biggest concern will be internet rights or electronic rights to your work. You have to consider licensing issues like e-books or maybe even newer technologies that may come about for the next ten years (hologram publishing?, who knows?) Even then for present time, movie rights, audio books, theatre adaptations etc. are major concerns to your work. Just being an artist and wanting your work to be publish is one thing but please consider the other avenues of your work.
Hope this helps. Again, this information from an author who writes science fiction. Some of the thinking still applies to regular fiction.