Right now the rear of the car is on jack stands and I'm taking out the floor and braces. Should I put the tires back on the car and lower it to the garage floor when cutting out and welding in the new floor pans?

Keep the car as flat or normal level as possible. If you lift it it might tweek a little. So leave all the weight on the wheels. So that when you weld it stays that way.

Sounds good, thanks.