Coyotes are sleeved. They're just thin sleeves. Only the GT500 uses the plasma bores.
This.
The bolts that come in the new block have already been torqued. You'll probably want to order a whole new set. They torque them down to spec when machining the block.
I recently built a '13 block and ran into the same issues as the OP. The 11/12 and all prior modular blocks have the head bolts thread deep into the block. The '13 block is much like the old pushrod blocks where the head bolt threads are just below the deck surface. Head bolt torque spec's are slightly different as well (18lb/ft, then a 180 degree stretch).
Here are the two head bolts: