92 Geo metro will not time???

I changed the head on my 92 metro and I align the marks at the crank and cam in the up right positions but the distributor is not aligned to fire on the first piston?

I for some reason have two marks on the overhead cam pulley. One has a little nipple on it along with the mark. I figured that has to be the right one, but it will not fire. Then, when I align with the other mark a quarter of the pulley around, it will start but run bad?

Any help would be greatly appreciated. The car was running fine except for a miss and low compressionin one piston before I changed the head.

the mark that is straight up when cam dowel is straight down is the correct one. when you pulled head off was one valve bad? might run compression again and make sure its ok in all the cyl. should be around 170