Timing gear marks don't line up.

[Ayers1]

A few weeks ago I had posted that I was having issues trying to get my car started for the first time after being restored. The engine was rebuilt by the previous owner and I pulled it while the body was off and checked clearances etc. While I was trying to get it started I found that I had to time it about 180 degrees off. It ran but that's all you could say for it. Finally got time this weekend and pulled the timing covers off to see what was happening. What I found was that if you line the marks up on the crank and cam gears, the piston is ~1inch below the top of the cylinder. If you bring the piston to TDC the marks are about 2 teeth past lining up. I bought 2 new gears and the marks are in the same place as the old ones. Has anyone seen this before?
Thanks,