Tell them you have a friend who is a cranky old suspicious guy who has taken apart a few hundred motors.

First, in exactly what manner is the manifold damaged/ruined now? IF it has a miss due to manifold damage, it can only be a vac leak on one runner of the manifold. The possible native leak sources are the head/lower manifold joint, and the lower/upper manifold joint. Both require a failure of the gasketed union. The possible third source is the changeover butterflies in the intake runners, most likely the end bushing on #1 cylinder, or #6, as leaks on the inter runner bushings only lead to more mani vac, and not atmo pressure. It's leaking enough to leak out one cylinder to the point of misfire around idle speed, and perhaps starts to fire at higher rpms and airflow in the runner, which reduces the effect of the leak relative to the increased overall flow in that runner.

It's possible you had an already worn outer bushing which got knocked out by the removal procedures. It's possible they dropped the intake and bent something.

All these manis are dry, except perhaps the lower, so there is not likely any corrosion damage.

One note. It's somewhat difficult to get the lower intake sealed to the head air and water tight. I used Indian Head or KopperKoat or similar copper bearing gasket sealer on the head around the ports, lower the same, and a coat on both sides of the gasket. Carefully set the lower intake in place when the gasket goo is tacky. Set the fasteners finger tight with moderate downward hand pressure on the mani. Set the torque wrench to half spec torque and torque all the fasteners. Rap the lower intake with a soft faced hammer or hammer and wood block to settle it into the vee evenly. retorque to 75percent of spec, and repeat the hammer blows. Repeat to final torque all steps. I use the same sealer on the upper/lower joint gasket.

I think their prices on the original work were fair, but I have a large question about the replacement manifold. The proce quoted is suspiciously close to the cost of a new upper intake with new butterfly shaft bushings...