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If you've used this boiler in heat mode for a period of time with the new parts and the same intermittent problem persists then I'd suspect the control board. The ignition function is the same for heat and hot water. The only difference is the mode that generates a call for ignition. That would point to the board.
At this point it's your next move unless you can catch this unit in the middle of a failure or you're getting an error other than ignition failure. Since it's intermittent catching it is unlikely. So far you've followed the procedure we would follow with an intermittent fault that evades diagnostics which is replace the least expensive possible culprits first.