Update: 1-14-15
Just got off the phone with Hot Rods. They concluded from their engineering department that they did in fact have a small batch of stroker cranks go out that didn't have the crank rod fully machined out on the sides of the lower part of the crank rod like they should have been. This can be seen in the pictures I attached and described earlier in this thread. They thought they had caught them all before they weren't out , but apparently some of them got out. So, if anyone else happens to run across this issue, hopefully they will take notice of this thread.
Now for the more interesting part, Hot Rods stepped up in a redeemed themselves. They were shipping me out a new crank with the correct machining and are sending me a return label to get this old incorrect one back on their dime. But that doesn't cover the money it cost me for the gaskets to put this engine together or paying my builder to install the crank and assemble the bottom end. So to help compensate for that, they are also sending me a full gasket set with the new crank, and sending my a bunch of Pivot works bearing kits to help offset my costs for the builder. They said they weren't able to send out actual money to compensate but could sent out some merchandise. I was surprised that they were willing to help make this right. But they did. In my eyes, they have righted this mistake and I am happy with their response.