First of all, sorry for your misfortune.
I am Critter on this one! I would never think of reverting all the suspension and parts just to get my dealership to do "warranty" repairs... It's wasn't stock when it broke, so... take your chances. You might be surprised!
My local dealership has already told me that as long as I do not do anything "crazy" (NOS, etc) that they would try to help me the best they can. We even discussed Forced Induction vice my NA and after-market tuning. They are willing to cover most modifications as long as it is not being "raced" at the time of failure. (>stock redline) It all depends on how good of a relationship you have with your service manager/dealership.
Remember: It is hours and money for them to do the swap/rebuild. It costs them nothing, all put out by GM. However, GM requires paperwork to release parts and labor money to do the work. SO... like everyone else says, it's up to the dealer/shop (and their level of integrity)
We have suggested this to a lot of customers, talk to the dealer that you work with and be upfront with them, let them know before you make the mods to the car and see what they think before hand, that way if something does go wrong like this, then you have a general idea of how they are going to react.
Considering that you changed the intake, tune, tubes and intercooler on the car there is a very good chance that the mods you made may have caused the failure of the engine.
As for pulling off everything and returning it to stock to see if they will warranty it, that is a personal decision that you have to make. It is a real bummer that your engine has been damaged, but going back to the dealer and not giving them the full information and asking for them to pay to fix it does not seem right either. I have to agree with Critter and some of the others here, if you want to play, you have to be willing to pay. If you want factory warranty, run factory parts. If you want to make the big numbers then be willing to take what may come with that.
If you do need some help though getting the engine back together, pointers or advise, do not hesitate to ask.