Hi Deltic,
My experience is only of stationary steam, but I have got stephensons gear to work but only on a single cylinder. There are three adjustments:
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The position of the eccentrics relative to the cylinders (typically how many degrees advanced from 90 degrees to the cylinder cranks).
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The alignkent of the valves with the ports.
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The set up of the link .
I'm assuming everything turns freely, you have roughly set the valves and the dimensions are OK?
If you have NOT set the valves relative to teh prots then this is the problem and we can help with doing this .
If the valve events are vaguely correct then it should work, albeit in a 'lumpy' or 'only with help' fashion until they are set closer to where they should be. I assume you have checked that the valve ports just start to open as the cylinders approach top/bottom dead centre.
When you ask about which side the eccentrics can be, I wonder if you have one pair the wrong way round.
Essentially each eccentric pair needs to be set so that at one extreme of the gear or the other only one eccentric from each side is operating. Make sure that in full forwards gear the 'active' eccentric for each cylinder is actually trying to turn the wheels the same way. If one side is forwards when the other is reverse you will get the symptoms you describe.
Neil