Dan,
Sorry about the description. These things are difficult to explain without pictures. However, I'm going to give it another go and address it in terms of what you could do to check your machine.
First you need a straightedge that is long enough to span the width of your machine. The reference surfaces you are going to measure are the black aluminum plates that are bolted to the linear rail bearing blocks. They are the same plates your gantry bolts to. Let's call them the gantry mounting plates.
With the gantry removed, orient the straightedge across the width of the machine. You place it on top of and spanning the left and right gantry mounting plates, just as if you were mounting the gantry itself. If the straightedge sets flat across the plates, then the frame is fine. However, if the straightedge rests on the outside edges of the plate, leaving a gap under it on the inside edges, as with mine, the frame rail that the linear rail mounts to is necessarily tilted inward. If the straightedge rests on the inside edges of the gantry mounting plates, leaving a gap under it on the outside edges, then the frame rail is necessarily tilted outwards.
When I refer to tilt in one direction or the other, there could be multiple causes, but the effect is the same. the whole side could be welded to the cross pieces at an angle, or the short vertical pieces could have been cut at an angle causing the top frame beam to be welded at a tilt (e.g., if you cut the vertical at a 5 degree angle, what should be the top surface of the top beam would be sitting at a 5 degree angle as well and would account for a gap on either the inside or outside edge of a gantry mounting plate, when the gantry, or some other straightedge, is placed on it.
I believe we have all been operating under the mistaken assumption that the problem must be with the gantry. We've all read that the frame is jig welded and stress relieved, so we just don't tend to go to the frame as the problem. It's just easier to conceptualize the problem as gantry related and go from there. However, I believe, and it has taken me sometime to get there, that the frame may be the culprit. That isn't to say that the gantry doesn't have problems - I don't know whether or not it does. If the frame is fine, then the problem defaults to the gantry. It's just that what seems to be the obvious answer isn't always the correct one.
I hope this better clarifies things. If not, I'm sure photos will make it crystal clear.
I'll let you know when I hear from Nate. Lack of contact is not an option.
Gary