The problem you have there is you are probably not going to find what you want for your budget.
Your list of requirements was pointing my suggestion towards a four thirds setup, however for $1000 dollars you would be very lucky to buy a camera and lenses for that let alone ports and strobe/strobes.
My advice would be to decide what sort of pictures you plan to take mostly. If it is macro Canon do some great compact options with the advantage of wet lenses for wide and macro.
Think about the conditions you will be diving in.... If you need a focus light. I only tend to use one if it at night or conditions make it seem that is night! More important are strobes!
I am not sure of the housing you have mentioned but be wary of going down the cheap route.... You are in a very unforgiving environment and even when care is taken they can take a beating in rough conditions.
Most people have a similar decision to make but there is not one easy answer (other than wait longer to save more!) to achieve what you want for the budget you have.