I wouldn't be too concerned until you've added the engine and interior and drove it a few miles. It takes that long for a suspension to yield to the forces and settle to its nominal position. All suspension parts should be tightened with full load on the wheels. Until then, snug everything up and install all the parts, and you'll find the suspension has dropped an inch or more. Then go for a ride around the block 2-3 times. When you come back, you'll find the suspension has dropped quite a bit. Get under the car and torque everything to spec. Until then, you can't be sure of an offset from side to side, as it could be due to how you tightened the suspension bolts without the proper weight distribution.
On my 66, it was 4-6 inches above nominal until I installed all parts, and it dropped only 2 inches. I took it for a 2 mile drive, and it was within 1/2" of where it should be. I was concerned as well, but everyone including Eaton said not to worry.