Like so many here I am no expert in the finer points of engine building, but your comments gave me reason to speak.
If you bore a 390 to get 427 you will probably have the same problems that Ford had with the "Center Oiler 427". That is, as I under stand it,
oil starvation of the main bearings at the high end of the rpm band. Unless, of course, you provide additiional
oil capacity to the mains, cross drill the mains and drill the rod throws for
oil passages, like the 427 S/O.
In addition, without significant head work, the breathing of a 390 might not perform up to expectations for a 427 displacement.
If there is a thin spot on one of the cylinders, at the bottom of the bore, is it below the ring travel area? If so it won't have much affect on it by the cylinder pressures.
If that area is above ring travel it, might not have that much negative effect due to gas pressures any way since it is at the bottom of the piston travel where the pressure is less and near where the exhaust valve opens to relieve the pressure anyway.
Is the 0".004 that you are talking about in the inside or outside of the cylinder liner? If it is on the inside it will "go away" when the surface of the cylinder is bored.
Realistically, does a quarter size spot that is 0".004 thinner really make that much difference? Chances are that if you build this engine, and then (heaven forbid) you blow it, that it won't be the thin spot in the bottom of a cylinder that is the major cause of failure.
But again, I am no engine builder.