I completed my -4 quite a few years ago, so keep that in mind as you read this post.
The F-406 bulkhead is the rear spar carry thru. First and foremost is to locate this so it fits your wing. I agree that F-405 appears to be located 41-5/15" aft of the datum, but believe that dimension is 5/16.
I believe the F-405B angles should be located 41-5/16" aft of the datum. There is no (direct) reference from the F-406 bulkhead.
All bulkheads should be located to provide a fair surface for the skin. This is more important than any dimension in the plans.
The RV-4 plans were drawing before sophisticated 3-D CAD tools were available (to Van's). As a result, not all dimensions are perfect. It was quite the norm for -4 builders to build the fuselage to be fair rather than compliant with the drawings.