My mods were not done in any particular order....due to availability or because I couldn't decide on what I wanted. And at other times, a better idea hits you later on and pushes your completion date back even further.
I would say though...pull engine and tranny first. Widen tunnel if necessary, fix underside and engine bay rust, do brake and fuel lines, engine bay paint (mine is just black heat paint).
Put in engine and tranny, check ground clearances when doing coilovers, exhaust, etc. I don't know if having the engine in when the roll cage is welded in is good or not...if the car's not level, it could permanently tweak the car?
I stripped my paint right after pulling the old engine...2 years ago...rust....
Owen