Am having a hard time believe this one, you have over 40AC output from stator, you fitted a new reg and the volts are the same has the battery...! did you check by putting meter at the battery (engine not running) make a note of volts, and again with engine running at over 3000 RPM.
If the battery is good.
You say there is over 40 volts coming from stator (a little high).
And you have fitted new Reg.
look at the wiring diagram and check all the connections, there are not that many.