I did see the color chart :) I have traced all the lines by color as well as by using the schematic plug connector chart.

Here's one of the answers I got:

Nope, not it ... but keep tracing.
A2J3-9 and A2J3-13 are the exact same signal on the rectifier board -- both are 43V out from the rectifier board. One goes to solenoid bus, other goes to relay (A3J3-5). If the two wires are reversed, it won't matter as they both come from the same place. However, for sake of tracing the machine at some later date - best to put the wires where the manual says they should be.

To me - it still sounds like a short between A3J3-5 and A3J3-6... somewhere. Not necessarily a short at the connector but somewhere in the wiring.