Best order for panel replacement?

Leaving the trunk in place is a good tactic. You are correct about the door hinges and door alignment. The fixed part of project is the quarters. You only need to be close with the doors in the beginning. After quarters are in place you can fine tune the doors. This is a tough job that takes PATIENCE. Everyone 's experience is unique to them. Ask questions until you are blue 'cause a lot of cars get ruined by people who don't get enough info