well.....I hate to say it.....but you said yourself they did mainly phords and chebbies. I would never have chosen them for even changin spark plugs on a mopar.
The fact that they primarily do Ford and Chevy work has absolutely nothing to do with the issues the OP is having. A reputable shop can machine and assemble a mopar just as well as they can a Ford or a Chevy even if they primarily do brand X work. The only thing a mopar specific shop will get you is knowledge of combinations that may get you more power.
moparmade43, Based on them telling you to keep driving the motor to seat the rings should have set off an alarm. If the bores were finished properly for the rings being used the rings are seated virtually instantly the motor starts and a good shop would know that. I would say there competency is not as good as the reputation they have.
In anycase you need to get face to face with the shop, keep a level head and work through to a mutually acceptable solution. All you can resonably expect is to return the short block to them and have them make it right and that is no different than anything you buy. If they truely care about their reputation they will go above an beyond to make it right and it is those companies that will cover the cost of labor for the R&R of their product when it fails. If they don't care it may take getting a lawyer involved but even that won't guarantee satisfaction.