I believe you have the angle strip on the wrong side. It should lap over the rear cross-sill. Swapping sides with your angle strips would make the holes match up at front and back with the other bed strips. The bed wood under the angle strip is secured to the angle strip with the bolts rather than with the center strips which use the notches in the boards to secure them. If the board widths are correct, they should match up with the holes in the cross-sills for the bolts and have roughly the same gap where the bolts go. It looks to me like on your second picture, that you have the outer board too far outboard. You should start in the center and go toward the outside edges, THEN drill the holes in the outer board to bolt to the angle strips.

You can see the overlap of the angle strips if you zoom in on the attached picture.

Moving your thread to Making A Stovebolt Bed, where it'll be more on topic.
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Kevin
1951 Chevy 3100 work truck
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1929 Ford pickup restored from the ground up. | 1929 Ford Special Coupe (First car)
Busting rust since the mid-60's
If you're smart enough to take it apart, you darn well better be smart enough to put it back together.