However, when i run string from the e clips on the left side of the limbs, my top limb is 1/2" longer.
If you are saying, the tiller is 1/2" longer on the top limb, with limb bolts bottomed out, then something is definitely wrong. Either you're measuring incorrectly or one of the limbs is off. Make sure the limb is seated in the proper position in the limb pocket, and that it is the exact length of the lower limb.