Check that the plugs are going to the correct cylinders, verify all the wires are properly seated on their plugs.
Verify the position of the timing belt (I'm assuming it was removed or untensioned when you replaced the waterpump and/or CHTS?) If its a tooth off on one side, or installed incorrectly it can cause this.
Verify the ignition timing is somewhere close to the spec for your vehicle, which should be printed on the sticker under the hood above the air filter.
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1985 300ZX n/a
See my Z project