I pretty much agree with the others.
I would price the service and the sub-panels and then do the rest at T&M. You have no way of knowing how long something like this will actually take. Make sure you put in writing that you're not responsible for any holes you have to make in plaster (unless you want to be).
Also, I would push the owner to completely re-wire every last inch of the place.
If she burns due to some old wiring they can come after you. It's better to just do EVERYTHING and then you're confident that everything is ok.
Square footage pricing really only comes into play with new construction. These remodels are often difficult because you never know how things are framed and you may not be able to fish the simplest looking wall without alot of effort.
It's got to be T&M or you're taking a gamble.
I usually get 50% deposit/expenses up front at time of contract signing, then 25% when substantially complete (especially if this thing will go on for months) and then 25% upon completion.

The way you're doing it sounds ok and if you run into no big delays you may make more $$$ than if you T & M it, but it is a gamble; you might win you might lose. I don't mean you'll lose $$$, but you may not make as much (which to me equals losing money).