Well, I thought I could return the frameset for a refund, but it turns out that one of Felt's rep's insists that 3mm out is acceptable, AND, if I return the frameset for them to jig, and it's 3mm or less, they will not refund, exchange or pick up the shipping fee. How's that for service!

So, the question is:
1. What measuring method can we use to verify alignment?
We did a string method, (bike in stand, wheels in place, place string around headset spacer then run each end back towards the drops and lace in-between each sides of each rear wheels axle nuts and dropouts contact points). It's a straight unobstructed route, both sides.
Then we measured the space from the seat tube to each string (left and right side) and sure enough, the left side string runs about 3mm more outboard then the right side.
Next, we installed the crankset and measured the gap between each crankarm and chainstay and again, the left runs about 3mm more gap then the right.

The problem is though is that it's difficult to know just how accurate that particular string method is when used with a carbon bike's carbon seat tube.

Another option: Remove the crankset and cups, place a long straight edge ruler on bb shell, point straight edge vertically past each string, then measure the distance from the string to the straight edge, both sides. Would that be considered an accurate method, or is there a better way?

We need definite proof that the frameset exceeds Felt's 3mm rule in order to refund or at least, exchange. (The LBS doesn't have a builders frame jig)

The gripes I’ve got are:
1) How closely the rear tyre tracks to the left chainstay – guessing about 3mm (I’ll feeler gauge it next) but it’s so close that I can actually make tyre/chainstay contact by lightly squeezing wheel and chainstay.
2) That the caliper’s mounting hole is about 2mm off the tyres center.

Does this whole alignment issue seem like a legitimate gripe, or, is such really nothing to be concerned about?
I’ll also ask the LBS to ask Felt’s rep to indicate what exactly does the 3mm rule include, and how do we measure such, just the same. And I'll finish buiding it up and do a test ride, too.