The rear scope rail you sent the link for has a windage adjustment. Did you try re-setting the windage turret to the middle of its range and then BORE SIGHTING the scope while adjusting the windage adjustment on the rear base ?
Just so were clear: Remove the bolt from the rifle. Put the gun into a bench rest or gun vice, pointed at a small reconizable target at about 25-50 yards. Center the target in the bore when viewed from the bolt position. Now peek through the scope without touching the gun to see where it is pointing at.
If I were you, I would center both turrets on the scope. If you read the manual, it will tell you how much travel it has in each axis. Then dial each axis until it (gently) reached the limit of travel one way. Now, taking note of the number of minutes per revolution of the turret, rotate it back half of the allowed movement. If you did not re-set your turret you should be close to the "zero" point on the turret.
Now adjust your scope base to get the scope pointed at the same place the barrel is pointed in windage.
I have never heard of someone stripping one of the scope base threads in a receiver. Often times, on cheap chinese made scope bases and rings, the screws themselves will be made of very soft steel and they themselves will strip easily.
If the thread really is stripped, they you have to go back to your smith again (this time take off the scope and bases yourself beforehand) and get the factory holes all drilled and tapped to the next size up. Buy yourself a steel one piece rail (picatinny style) and have him open up the counter sunk holes in the one piece base for the same screw size. If it was me getting this done. I would have him drill and ream and pin the one piece base to the receiver at the same time. That way it will never move on you, no matter what.
Usually, smiths charge about $15/hole so 4 holes should cost you $60 + 2 dowel holes will be $90.
Don't waste your time with micky mouse scope mounts when you put so much money into the optic to begin with.