I would start on one side and do a quarter and wheel house on that side, do the other side next, then work the floor and tail panel. These cars have no seperate frame and rely on the body panels and the welded in frame rails to support the rear of the car. You don't say if your doing inner and outer wheel houses. The inners add lots of support due to the tie ins to the trunk hinge area, floor behind the rear seat, etc. Weld as much of that area as possible before you move on to the other side. Leaving the old trunk floor and tail panel till last will leave some means of support while the quarters are removed. Remember, one side at a time though. You can also use extra jack stands or build some wooded supports to place under the old rear panel to keep it from sagging while each quarter is off. Be ready for more rust and carnage than you can now see. Good luck
Give the laziest man the hardest job and he'll find the easiest way to do it.