Your bearing does not look right. I just went and looked at pictures from my rebuild and your bearing does not appear to be not aligned.
I suggest you call Matthew Kenney (805-238-0912). He owns/runs Aircooled Research and specializes in 36HP engines. Could call Joe Ruiz (Mr. Okrasa) as well. Shoot them a picture.
Also, 36hp rods do not self align like the late model engines. I doubt your rod was wrong, it just wasn't aligned...I went through this same headache with one rod on my engine. When you torque the rod bolts do them in stages, at each stage slightly tap the rod with a hammer at the joint of the rod halves...this assists in getting them aligned. Others use feeler gauges between the rod and crank.
Speedwell USA sells Okrasa intake manifolds for dual 2bbls (IDF's and DRLA's)
Picture of my engine...same half you show:
Dual Carbs: