I always dread the senarios where you start of with an existing city that is almost in ruins and really not planed correctly. I guess its because I usually end up paying to much attention to the old city instead of concentrating on the immediate manors at hand. That's why this city was hard for me. I actually ended up restarting the city three times. What adds to the complication is this is actually a military campaign and you almost need to forgo rebuilding the city and think about defense almost immediatly. With that said here are a couple of points that worked for me.
1) Begin by boostering the defenses of the old city.
2) I then started my new city on the Eastern Island. Concentrated on gold mines, exported copper, and surplus fish. Used the small island as a location for a lot of the fish wharfs.
3) Beef up your army quickly and make sure you have at least 3 transports by 1944 BC.
4) I created the Temple Complex for Seth, but looking back I wish I created the complex for Osiris. Did not get much benefit from Seth even with the temple complex.
Used 23 x 8 housing blocks with a pavilion, bandstand, and booth on three of the corners. Also take a look at the entertainment center just outside the old city. It's made up of 4 pavilions.