just like a house..the foundation comes 1st, get the chassis sqaured away on your fixture, then have the car sitting with suspension loaded for optimal panel alignment.
lots of time, lots of trial fitting will be the key, cleco pins or self drilling screws will work wonders while trying to fit all the loose parts together....especially when replacing the entire back 1/3 of the sheetmetal.
good luck...and its not too late, sell the car and buy a bass boat...no poles, all ya need is the boat and beer.... it will be cheaper and much less headache