Anyone here dealt with a similar issue?
YES!
I had the exact same problem. I found it out before I assembled my cases. My first crankshaft was factory assembled. When I removed the bolt in the front to add Loctite and re-torque I found the bolt to be completely stripped. Upon closer inspection I could fit my fingernail between the prop hub and the oil sling ring on one side. After contacting Sonex, they had me get it back to the factory for correction. They claimed to have fixed it and shipped it back to me. The shipping method Sonex chose made me question how straight it was (single layered cardboard box and virtually no packaging paper-the crankshaft busted through the box at both ends and was partly exposed when found at my door). Sonex claimed it was ok to assemble, but I wanted to know for sure. So I supported it from different bearings in the case and spun the crankshaft while measuring run out with a mounted dial indicator at several locations. While doing this my prop hub contacted the case in the same exact spot as yours making metal shavings. The dowel pins where not a factor on my set up as I tested.
Getting back to the run out. The crankshaft had significantly less then 0.001" (the scale on my measuring tool) no matter where I measured it on the journals, but the prop hub was not so straight. In the area that the hub contacts the case my hub has a radial run out of 0.012" The face of the hub that mates to the propeller also has significant run out. The run out at the face of the hub in the axial direction measured as far out on the face as possible (about 5 inches on diameter) is 0.007" These numbers were provided to Sonex. They asked me to measure my crankcase bore at the prop hub opening. Mine was 2.204" on diameter. After telling them 2.204" they asked for both my crankcase and my crankshaft back for closer inspection.
Sonex gave my parts to their machinist. The solution by their machinist to this problem was to enlarge the opening on the crankcase where the prop hub goes through. After the machinist took measurements they said the hole was slightly undersized and off-center. They claim that the hole is now enlarged to the correct size and re-centered. I have not been able to verify this yet.
As far as the run-out of the prop hub, according to Sonex, my run-out is not a problem, and is "within their tolerance". However the only tolerance I can get then to commit to is that the face of the hub, measured in the axial direction at the 5 inch diameter is 0.010" or less, making mine at 0.007" ok.
I would be curious as to what yours numbers or anyone's AeroVee for that matter are if you measure run out and the crankcase bore diameter at the prop hub.
For reference, my engine was purchased November of 2013.