I recently discovered a leak coming from the timing chain cover. I have everything tore down and also noticed a fair amount of play in my chain. 220k miles. I began re-assembling things and started to question myself on the timing. Before removing the old timing components, I made sure TDC on the balancer was lined up with the timing mark on the cover. After removing the timing cover, I noticed the marks on my gears are not side by side. They are in line, but both marks are in the 12 o clock position. My question is do I need to find TDC on the compression stroke in order to ensure things are correct, or would it be fine to replace with the way it currently sits? I appreciate the help in advance

 

If nothing was moved, and the marks are both at 12 o'clock you should be fine.
That is just telling you that the engine is set at the opposing cylinder. Might even be a #1. Not sure about the ford, but GM used both gears at 12 for a long long time for #1