Like the saying "how do you eat an Elephant" with the answer "one bite at a time", tackle the car. Its easier to keep control if you do an area/section at a time. If you plan on upgrading suspension/brakes, wait until you have all the items in hand, then get after it. Do you have any floor pan/trunk rust to deal with? If you do, the interior needs to come out for that job. So, what about replacing the carpet. any upholstery work, frame connectors, wiring upgrades/changes etc in those areas? You'll want to address stuff like that when you are in a given area as its out and you are already there. Opposite of the thinking states/municipalities do when the re-surface a road then come back in to put underground utilities in and jack up the road. For my stuff, I start at the inside areas first and cut those down to sections to tackle. My car is mostly gutted and I'm dealing with engine compartment first. When it gets closer to paint time in that area, I'll pull the doors off as I'm going back to the original color. The jambs will get stripped as will the back of the doors. That way those inner areas are already done, paint wise and I won't need to pull the doors later for paint. When those areas get dealt with, I'll get into the middles of the car to do the structural upgrades. Frame connectors, torques boxes etc. There will be some overlap into the back area so the cut/modify/weld operations will all be done at that time. Cuts down on re-do's. Your outer body/paint stuff, to me, should be saved for last and not done a piece at a time spread out over weeks/months/years. Like painting a room, start in the back and work your way out, not into a corner.
