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Most of the guys in the forum use a thermal gun, to read the heat output of the cylinders. If one is hotter then the other, you can loosen the IP for that injector, and turn the IP left or right to adjust the output of fuel to the hot cylinder. If one jug is hotter then the other, its working...
All military gen sets that are "water cooled" run at 180-200 degrees.
First get everything fixed, then we can try and suggest a few things to look at concerning vibrations. There is not much to be done, but a few things to check.
While I was writing, Ray took the words right out of my mouth/fingers. Next time, only remove one pump at a time. Its a lot easier to get them back in right that way.
If you got the pumps good and clean, there is a way to get a feeling as to if the pumps are seated right. Loosen up the clamps...