Rather than valve cover rail or modest port misalignment, another, or perhaps the bigger issue is how well the mounting holes line up. Assuming the heads and intake are at or near OE spec dimension, is the reason the valve cover rails are low due to rail height merely being machined too low or has more/incorrect amount of material been machined from the intake faces? Or was the intake intended to use a .125 gasket (seems unlikely). You do have a standard thickness head gasket installed....correct?
Increasing the intake gasket thickness .062 will raise the VC rail the same, but it will also move the mounting hole locations on the intake in respect to the head, somewhere between .062 and .062/sqrt2 depending upon the angle of the hole. A vertical hole (45 degrees to head face) won't change at all.
Unless the mounting holes are grossly over size, that is likely greater than the radial clearance of the intake mounting hole to the bolt, so that means your intake could land on the sides of the bolts before it seats on the gasket..........very bad......no seal.
Before you buy a .125" intake gasket, see if you can install mounting bolts with your present gasket, and then do same with two .062 gaskets.
Best,
Kelly