I'm a fan of pulling the engine for heads/gaskets. IMHO, it's easier that way especially with studs.
The studs should not be torqued down in the block, just tight enough to seat them fully into the threads. It is normal for a few to come loose as you untorque the heads by reversing the factory sequence.... no more than a 1/4 turn at a time. If you just start loosening the nuts on the studs randomly, you can warp/crack the head.
Also, when you are done, you should repeat the 80 ft/lb step (4th in the torque sequence) until not a single nut on the studs moves when applying the 80 ft/lbs of torque. If any of them move, repeat the sequence again.
Get a tube of ARP's fastner lubricant and coat the snot out of the threads, washers, and nuts before torquing them down.
Heath