Ricki,
Sorry that I'm late to the party, but I did come across a problem that I think everyone has missed. Your trying to mixed rods and valve gears from different eras, especially the eccentric crank. Lionel faced essentially the same problem (rod clearances) when recreating the 700E in 1990. Their solution was to create an offset of the arm on the eccentric crank. Jeff Kane bought a number of these eccentric cranks and sold them as 700E parts, when in fact they were not backwards compatible. I know because I created the comparison years ago. See below. 
This offset allowed Lionel to create the side view illusion that the rod configuration was the same as the original 700E, however one only needed to look from the top down to see that the rods were not running parallel.
