RE: Two bolts on main shaft.... special steel or not?
Welcome!
Cheer up Firefli! It's all part of the learning curve! we've all been there and done that - and will no doubt do it again!
From what you have described I would say there is a 99.9% chance you have sheared the two screws off in the main shaft. It is also feasible that the is a remnant of each left in the holes and that would explain why you can't see daylight. You will need to shine a flashlight into the holes until you see the shaft holes line up with the gear holes then punch them out with something 3mm or less in diameter. The shearing forces leave burrs that retain the remaining portion of the screw.
It is also my educated guess you have bent the feathering shaft as well.
You will see from my note above that I am still perplexed as to why e-flite don't supply the two M3 x 12 screws with the new shafts (it's a screw because the thread goes all the way to the head - bolts invariably have a plain part of the shank to the head). You get new screws with the feathering shaft each time but they don't bend! I disassembled the heli not so long back and one of these screws was bent and I didn't hit anything! To get these you have to buy a complete hardware set unless you can find a supplier.
Have you also checked your servo gears? Tail shaft? Fly Bar rod... all the usual suspects for blade strikes.
Jon