Welcome to the forum.
You didnt mention anything about the bike being a runner, but too late fir that as You have already the bike stripped down to the frame. Just clean it up and attack a small system at a time. Save the parts that you feel not going to be use, but might need them later.
While I would do in this order, and other may do it differently.
Frame, engine, wheels, electrical, then air and fuel. Once your bike is going, let's make it stop, the brakes.
Good luck