I wanted to give everyone an update.
After speaking to about three different mechanics, we decided to just swap out the gasket and see what happened. Our plan was that if this failed, we would then try a liquid gasket, and if that failed, jbweld, and if that failed, actually welding the case.
So, after just swapping the gasket our for a new one, no leaks! So that is good, and everyone who suggested that the damage didnt go all the way through were correct.
We only have about 30 miles on the bike so far, and we are keeping our fingers crossed, but everything is running tip top as of tonight.
Now, moving on... one thing that didnt sit right with me during this whole fiasco was how the problem occurred in the first place. Now I am not a real mechanic (i.e. get a paycheck for being a mechanic), so I can understand if I make a mistake and I can live with that (God knows I make enough mistakes). But with this particular problem there were two pieces of metal on each cylinder head. Each piece of metal was exactly the same size and shape. Each divot left in the crank case and cylinder head were exactly the same size. Each divot was spaced exactly 5/8" from the corner bolt hole on each cylinder head.
So there were two spots that were damaged in exactly the same way. The probability that I could have screwed that up is crazy. I dont think I could do that if I tried to.
I would suggest that if anyone does this mod, that they inspect their parts before putting them on the bike. I cant help but think that these pieces of metal that caused the damage originated from the big bore kit (either the gasket or the cylinder head). I know that from now on, I will inspect very carefully any gaskets or parts that seat/seal for fit and abnormalies.
Again, I would like to thank everyone for their help and Ill try to give another update in a few hundred miles. Without your help, we wouldnt have had the confidence to fix this problem ourselves (and would have spent life changing money getting it fixed).