Everything should line up when the cam lobes on the #1 cylinder is pointing "away" from the piston - this is TDC on #1 cylinder. If you are able to rotate the engine through multiple cranks that tells me that it sounds like everything is probably ok. You would not be able to rotate it if the timing was wrong because the valves and pistons would be in the same place at the same time. If I remember correctly the #5 piston and # 1 piston are at the top at the same time but only one of them is at TDC compression at a time.

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Jim