Goofy Thrust Bearing Gaps

Did you give the crank a tap with a hammer on the snout (to send it rearward) and then on the flywheel end of the crank (to send it forward, this being the desired end result especially with a standard transmission), (with the torque spec of the thrust cap tightened just enough to hold it in place) this should help "set" the thrust to the location it wants to be at. Then tighten up and re-measure.