Civic definitely does come with an immobiliser, and it would be lovely if you can have a working one in your car too. However looking at the tragic state of affairs your wiring is in, it seems quite improbable that it can somehow be fixed end to end with perfection, just the way the manufacturer intended.
Anyway it is now up to your own expertise to ensure that every single wire is sorted and taken care of. For this you will need to have the schematic with you and you will have to dictate it to the illiterate electrician what to do, otherwise you will have all sorts of problems since your engine is VVT.
Lastly, it would have been best to leave this car in its original condition and to give it a wash and polish on weekends, to connect more with the memories associated with it. What you've done with it now will probably drag you to mechanics on every weekend, for one thing or the other, till you get fed up of that exercise and decide to part ways with the car.