Unless you plan to be a road warrior, don't leave a stable job to be a contractor. Hiring contract engineers is not the same as hiring engineers. As soon as this project - or your involvement in it - is over, you are out of a job.
If they are telling you 2 -3 years, you won't even get per diem or reimbursement for living expenses. This means relocate or have two residences at your own expense. Not impossible, but not ideal either.
Forget raises. You might get one when you go to the next job, but almost never during one.
As far as altering the contract YOU WON"T HAVE ONE!!! The word "contract" refers to the agreement between Duke and Aerotek. Duke can literally micromanage your hours and when and for how long you will be there (depending on the type of contract they have) and send you packing at will.
Of course, these are all generalities. You should ask Aerotek to give you a written contract, and ask them to put these things into it -- such as guaranteed minimum payment, relocation, etc. Who knows? Maybe they will. If they don't, however, your employment will be totally at will (meaning at the whim of someone other than you).