Let me get this in my head straight.
You take the rifle which shoots 1/2-3/4" groups out of an unbedded wood stock, put it in a synthetic stock and it shoots 2+ inch groups.
Then you take it out of the sythetic stock, put it back in the wood stock and it shoots groups larger than 4 inches.
Now you bed the rifle in the wood stock, change scope, and de-copper it, and it is shooting about 12" groups?I suggest you put the old scope back on and copper it up.
your rifle should not have shot so crappy when you put it back in the wood stock in the first place. Something was wrong back then. Cleaning it obviously didn't help, neither did the replacement scope. I am thinking something is binding really bad or the crown got goobered up.
I suggest put the old scope back on, put it back in the wood stock, make sure the guard screws are not hitting the bolt. and shoot it again for some groups. Let it foul and see if the groups get better as the rifle gets dirtier.
BTW, was this rifle free floated in the wood stock before it was glass bedded. After it was glass bedded was/ is it free floated.
As posted above if a rifle is bedded in a bind, that is not a good thing.