We did look at the spokes. The wheel needs to be trued but everything looked OK.

They have gone above and beyond to resolve the situation. The free items would be the front derailleur (which I had just purchased but was refunded in full), the chain and the chain ring. The rest of it us just replacing the damage that occurred after the initial work. The bar tape was certainly still usable but I'm glad they are replacing it as well.

I actually just received a call from the shop with an update that it should be ready to be picked up this evening. Now, I'm just hoping that I receive a dialed in bike. I will likely have it looked over at my LBS as recommended previously.

Thanks for all the input gang! I do have a work stand and have started to do some basic stuff myself but I have a long way to go. I'll update again once I pick up the bike...