At this point I would carry that block down to the machine shop and let them look at it.
It sounds like a very poor job to me.Or they just had the caps in a different order.
This is why I don't like line boring. It takes a very knowledgable machinist. And the SBC rarely needs it.
If it is a bad job and they say they have to recut it, I would consider scrapping and starting fresh. Two cuts could lead into more trouble, especially if the deck was cut.
I would go with your instinct here, if you are feeling uncomfortable with a part of a job, then there is probally something wrong.
I would hope if the shop did do a poor job that they will do whatever it takes to correct it.
Keep us posted to what you find.