The fore arm of a lever gun and a single shot shouldn't touch the receiver. That presents a possible inhibition of the barrel to vibrate freely upon discharge. Accuracy is all about letting the barrel do its thing, and do it consistently.
Have you tried shooting it with the fore arm completely removed? That'll tell the tale of whether or not the wood is the culprit behind your awful accuracy. Mind you, the dynamics of the rifle changed a lot when you bored out the barrel and made it weigh a lot less than when it left the factory - it's vibrating/whipping quite differently now upon discharge.
Were it my rifle I would buy/make a new barrel stud with or without fresh 8-40 threads in it. (I wonder if whoever did the re-boring had the stud off and didn't get it perfectly back to where it was supposed to be?) If making a new stud without a threaded hole in it, clamp the barrel securely and level in the drill press or mill with the drill bit poised over the new stud, and then clamp the fore arm on where you want it to live on the gun. Run the drill down perfectly centered in the stock's hole and drill the stud. Remove the wood and finish the hole and thread it with the quill of the machine also. That way it can't possibly be out of alignment. If the new stud is already d/t'ed the protocol is much the same, simply use the new hole to center the bit and then stick the wood on to see if it hits squarely when passed through the hole in the wood.
Screws/bolts lengths are always measured to the bottom of the head, with the exception of flat head screws which are measured overall.
