Pros
Depending on who the client is you can negotiate the salary pretty well after being there for some time. Most of the clients will want you to convert to the government after 6 months of proving yourself. Your client overall is the one who will make it or break it for you at the navy yard. If you do not have an understanding and transparent client, you will end up quitting, its that simple. Code 50 (Control Systems) is worth working for over 40 (Power Systems).
Cons
Code 40 clients and consultants that get in the way. If you work in Code 40 you have to be careful with who you work for. There are some people that will make your life as difficult as possible and will make the environment hostile. Remember, this is government and people tend to become complacent, and comfortable after spending decades in the same position. There is a lot of red tape you will encounter and getting things done efficiently and on time are un-heard of. If you work for Code 40 you will most likely transfer to 50 and worse might even quit after the a couple scuffles with the customer.