If you have not already done it, you need to reinstall ALL of the sheetmetal,especially doors, fenders and hood to be sure everything fits as it should.  Once you get it all perfectly aligned, (and this part is optional but sure does help) drill witness holes through the door hinges, hood hinges and fender flanges into underlying body of the car.  A 1/8" hole will allow you to easily reposition the parts after painting by sticking 1/8" diameter cotter pins through the holes, eliminating the need to readjust everything.  The pins have a loop on the end making them real easy to remove.  A dab of seam sealer and paint will hide the hole, or you can just leave them there.

Before you paint the doors, wrap the window glass in masking paper and stick it inside the door so it is there and ready to go and you won't have to scratch up the door paint getting it back inside.  I would NOT use a plastic bag for this.  I learned the hard way that the plastic quickly develops a static charge and attracts dust to the surface of the door.  Same for plastic over the engine bay when painting a hood in place.  Plastic attracts dust to the hood in unbelievable quantities.  The transfer of paint from the paint gun to the car surface apparently builds static electricity.  Ground the car body.

I am assuming you have the mechanical details all worked out as to engine, tranny, exhaust, etc so you don't have to pre-install all of that before painting.  If not, it would be wise to do so.

After that, get it rolling, then engine,tranny.  Then interior.  Glass last.

I'm sure you will get lots of variations on plans to reassemble the car.  Just pick the best parts you like and go with it!

Just don't sit it in the garage and forget about it!

I have done several cars, and MS lays it out nice, and those 1/8" holes come in real handy, and no one but you will ever notice they are there. I havent ever laid the door glass in the doors prior to painting (dont for get to wrap), thats a great ideal.

Thanks for the guidance! Sometimes you get overwhelmed and can't see the next step.