Engine starting to settle down now with less over fueling, clatter - I guess switching out one set of delivery valve holders from another pump is not such a great idea after all, that said if you can put up with diesel clacking for a while the extra power makes up for it.
On the subject of wobble in case anyone is looking for other solutions, came across this video highlighting the crank sensor, if you look at the engine while running it too has a distinct 'wobble'.
https://www.youtube.com/watch?v=7LTN1PlhDOY