The solution comes by placing the rudder as ID2 in the Windows Joystick/Gaming Control Panel , and leaveing the Stick and Throttle (the BU0836 board with two physical devices attached) on ID1.
(The extra third party JoyID software was used to force the proper order of ID's in Windows.)
Then the following seems to work.
Device3 Port=3 could be a value Zero as well to turn it off, as its not needed.
Windows Joystick=1
Device1 Port=1
Device2 Port=2
Device3 Port=3
Rudder Device=2
Throttle Device=1
Stick Device=1
This may be the solution for some of the
HOTAS with rudders chain-linked, but dont want to work properly. EX: rudder axis seems moves with throttle device.
My theory is EAW v1.2 or in later versions, Device1 on port 1 can successfully hold two devices that are bound to the same ID1 in JOY.CPL. A third device is possible (like a rudder or throttle) when chain-linked, but better chance of it working with controller software with a legacy game option.
However some of the more tricky configurations that work in EAW, won't work with Modern Games properly. There maybe hope with additional software to allow modern games without legacy support built in, I'm looking into it now....
Anymore input from anyone experienced with these sort of things would help solve these type of issues.