I don't think $5K is out of line for a fully assembled and dyno tested and tuned engine with a warranty?
Yes, you could duplicate this for around $3,500? in parts and machine work, but you still need to assemble the engine or pay someone to assemble it, and dyno testing can be $500+, and you would not have any warranty?

I don't know anything about the shop or quality of work they do, which is a big factor. I would ask if they replace the rod bolts and resize the rods after, and what brand/quality of bolts used? Also, ask if they install hardened exhaust seats in the heads for unleaded fuel.
If you decide to use them or another shop that dyno tunes the engine, make sure the tune is done with the carb and ignition you will be using in the car.