As long as everything is in place with the locking tools the sprocket can be in any position really. On the chaîns there are colored plates that align, unless alot of parts are aftermarket and may not have markings on them.
As long as the camshaft is locked, the crank is locked (in the correct position), the only thing you need after that is the pump in its correct place. If the pump hasn't been de synced with the crank, the issue could be between the crank timing and the camshaft. One method would be to pull the first injector and drop a pencil down the hole. Turn the crank until you are sure the pencil has risen to its maximum height. Then confirm the crank position with the locking pin , then control the camshaft.
If it was out from the start there could be other things jiggered