If you're looking at performing an engine swap then the best thing to do is;
1. Repair the body/shell of all rust and damage and coat it in PRIMER and not the colour yet.
2. Mock up all the mechanicals; engine, transmission, cooling system, suspension etc. You don't want to go cutting/welding a newly painted shell.
3. Once you've got all that sorted, remove all the mechanical parts. Get the door gaps right, shell sorted and get it painted.
4. In the meantime work on refurbishing and getting the mechanical work finished for installation.
5. Interior, glass, trim, carpet and etc should go on last.
6. Drive away no more to pay hopefully haha.