The setting of the tappets shouldn't be influenced by how much the head has been milled, the adjusters will take up the excess. I THINK if anything the valves will open a little further with the extra milling of the head as the distance from the cam centreline and the pivot point of the rocker arms (rocker shaft centreline) has been reduced, i don't think this would be the case though if you've set the tappets again.

Have you checked if the pushrods are straight? Big spring pressures on the larger capacity A-series are a no-no as their pushrods are longer and therefore more prone to flex and bending. The smokey factor is an odd one though and sounds like it may be something else.

The other thing is if you have wiped the cam lobes...