Its how mine came back. I had the engine back from the engine reconditioner and I just set the timing gears running off the crank as per manual and added the pump, aligned the marks and it fired up straight away once the air was out of the injector lines.. Injection shop said they could make some minor adjustments if it smoked etc but it was perfect.
The part where you align the marks after putting the pump back on is the part where you're timing the pump...right?