Hey guys I need some help. I have an OS .40 LA, I took the head off to check the head gasket but when I was reinstalling the head the cylinder came out part way, I didn't think much of it at first but when I started tightening the head bolts I could tell some thing was wrong. I took the head back off to find that the edge of the cylinder was on top of the alignment pin and when I started running the bolts down the pin got pushed into the crankcase. There is just enough of the pin sticking out to align the cylinder but I am afraid the cylider might turn. How can I fix this?

Don't worry about it. If you have the cylinder sleeve properly lined up and the cylinder head tightened down correctly, the cylinder sleeve won't move. The alignment pin isn't to prevent the sleeve from turning, but to make it easy to line up correctly when it's installed.