With the kind help of the JMRI group I managed to solve my own errors in the preferences menu of the JMRI and successfully wrote the necessary configs like the address and the like to the engine via the write sheets panel without any errors.
I even disabled the first loco of the fleet from operating on analog power. It is my experience that analog power screws up the unit and requires a reset.
If I can do this, anyone can.
Let's see..
It was the RR-Cirkits Locobuffer USB that was purchased from Tony's Train Exchange recently and came with a USB cable, telephone wire and basically went straight into the Superchief without any further errors once the preferences of JMRI matches my connection on com 3 and properly talking to the engine.
I know that within a few days Im going to probably add a second engine and attempt to build a consist of two engines.
I think that I will just configure the second engine by itself, set the direction to reversed and MU it as necessary from the DT400.
Oh one other thing... this Proto SD7 was sooo new that it was not showing up on the JMRI decoder list. However it idented properly as to manufactor. That was enough for me to build a roster entry for it.