I bought used headers for my 260z and they seem to line up. The head is square exhaust ports so are the headers. The problem is the intake manafold is 1/2 inch thick and the headers are 1/4 inch thick. How does this work with the circle piece that holds both of these down and together.

That appears to be a common problem with some headers. See this thread for example:

http://www.classiczcars.com/forums/showthread.php?t=14869&highlight=header+mounting

I know it is from 2004, but the "solution" seems to be that you need to make or find stepped washers to make up the difference in height.

You need "Half Moon" spacers. It's basically a 1/2" thick washer, with 1/2 of the circle diameter shaved to 1/4". The 1/4" part is for the intake manifold side and the 1/2" side would be for the header side.

I had to use those on the 71' Z that I used to have. Worked like a charm.

Dave