318 Duster Rebuild - pros and cons of keeping matching numbers

I'm trying to wrap my head around your shop guy saying it'll be a better engine if you get a new one... There are no "new ones". What you'll get is a different engine that has been rebuilt, just like you want to do to your existing engine. Keep hunting to find a good rebuilder- talk to people at shows and members of local clubs to see who they recommend (or say to avoid!). There are good shops out there- but you may have to wait a bit in line once you find them- but that can also be considered a good sign, since their work is obviously in demand.
He's exactly right. I just got the call yesterday that I'll be getting my 65 Barracuda into the shop rebuilding my engine later this week. I waited four months. Good shops will have a waiting line.