As it always goes, you can have a "plan," but expect it to go astray. As you disassemble the car, you may find that it will need more work, or additional work, that you had not expected - so be ready for it. If you have a budget or time frame, throw it out the window. Just figure to spend what it takes and it gets done when its done. Then you won't be disappointed or frustrated.
You will be investing a good amount of money into the car, and not knowing its overall condition, you may want to go a few steps further than you plan. With the age of these cars, unless someone has already replaced a few things, you may find more than what you think the car needs.
I would pull the engine/trans and set it off to the side for now. Pull the interior out so you can check floors and the inside of doors, quarter windows, and rear package tray. You did not mention the dash, but often the area between the dashpad and windshield is prone to rotting due to moisture collecting in this area. Make sure this is solid. If you need to do any welding or sheet repairs, you want to do it with the interior, and possibly the dash/wiring removed.
With the interior removed, if the floors look solid, you can prep and paint them to protect 'em.
Next I would do any front/rear-end/brake/chassis work. Get this all done before any body work/paint.
If you plan on doing any work in the engine bay area, now is a nice time to do it with the engine/trans out.
When all this is done, then I would send the car to the paint shop. You want all your work done so as not to do any damage to the body/paint because some tool slipped and tore up the paint or put a dent somewhere.
When it comes back from paint, install the interior and at the same time send the engine/trans out for rebuild. You can be installing the interior with the engine/trans in a shop.
You really don't want to rebuild the engine and then let it sit in a corner. It's ok for a short while, but too long and you could have moisture get into the engine which is now bare steel clean inside, and have surface rust set in. Now if you are going to assemble the engine yourself, you can have the engine worked by the machine shop and have all your parts needed to assemble it ready to go, but don't assemble it until you are near ready to put the car back on the road. I have my 455 all in pieces, sprayed down with WD-40, bagged, and setting on cardboard to absorb any moisture. The parts also sit inside my house in a room to further protect from outside conditions. It's been 2 years and they still look like the day I brought the parts home. I will have to thoroughly wash/clean those parts I protected with WD-40, but this should be part of engine prep anyway prior to assembly.
So that is my recommendations, but you can do this in any order you feel works for you. You just want to minimize any chances of body/interior damage when doing any work after they have been done.