I'm not sure what you are doing, but if it is setting the timing, there is a mark on the camshaft gear that will need aligned. The same with the crank.
As far as your question, at TDC, the #1 cylinder lobes on the cam should be the farthest away from opening the valves as they can. If this is a timing issue, use the timing marks.
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Saturday, September 17th, 2011 AT 4:42 AM