Correct me if I'm wrong but it sounds like you haven't bought the car yet. In wich case I would just find one that is already a manual.
Doing the manual swap isn't all that difficult, its just time consuming. Their are a few people on here who have done them, myself included, so we can help you with any problems you run into.
To answer about the firewall, I doubt its punched. I had to drill the hole out, but honda outlined it already. Mine was done on an accord, but the preludes are very similiar in this aspect. Let me know if you want more info, because I found a write up that I can send you.