dgehricke,
Unfortunately, I have not been able to view your images so I must imagine what you are describing.
I also don't know whether you are asking about doing your boring on a mill or a lathe.
Excuse me if I am covering the obvious, but one must start somewhere.
In general, It would seem that you would make the bearing caps and mount them to their location before boring.
The general advice for a precision hole is drill, then bore with a boring bar, then ream.
If you have the holes drilled already, they would be undersized to allow boring. If you can locate the hole centers from either side (end?), then you can try setting up your part for boring, using whatever collection of clamps, anchors, blocks, shims, etc to do so so that you can then bore from one side. When I had to do this last, I used a known (and tested) bar mounted in a collet in my mill as a reference running through both bearing locations to double-check what I was intending to cut. I needed a long boring bar, which I assumed was going to flex, so cut in small increments with lots of lube and chip control and stops to measure.
In all fairness, what I was doing was also compensated for by the fact that I was going for bronze insets in cast iron, so the precision was in the I.D. of the insert, rather than in the I.D. of the bore.
I hope that this may be helpful.
I also think there are others who may have input.
Best of luck,
ShopShoe
PS: I just reread your post: I have assumed that your crank is straight. Is it possible that it is not and that is the binding you are experiencing?
SS