If this motor rotated fine before and all you did was change manifolds and such how does a piston all of a sudden be hitting the crank ?

I'm in the class of people thinking something isn't Kosher in Denmark here.

A Stock build should not need trimming. Combined with the fact the problem suddenly appeared there is something loose or wrong.

Pull that rod cap.

There has got to be something wrong to have only one piston hit because they all are the same and so are the rods and crank throws. For some reason that rod is shorter or the piston longer. Grinding is just a way to get the crank to rotate but it sure isn't going to cure the problem. It would be very bad finding the problem after reinstalling the engine and starting it.

Did you pull the right head? It would be interesting to compare piston heights. I agree with the others, with stock parts you should not have any interferences.