After attemting to set the cams and tighten journal holders over and over again I am stumped. Looking at the diagram pic the slots in the cams are supposed to face each other along with the #1 line flush with the cylinder head. However no matter how many times I try with the RT mark aligned with the pickup I cant get the number 1 line flush or the journal slots perfectly facing each other. Either the line is too low and facing at like 4 oclock or its too high and easily seen over the side of the cylinder head. Are my eyes just playing tricks with me, or am I doing something incorrect, I have literally attempted this 8 times with no success. I put it all back together with it timed to what I thought was the correct position and engine would crank but not start. even with starter fluid I got no response. I found a post similar to this on here where a guy had a similar problem http://gstwins.com/gsboard/index.php?topic=46666.msg523476#msg523476. What am I doing wrong, I think it may be one link out of time but it seems I cant adjust either way without it not appearing like the diagram pic on both the cam slots and the #1 line.

Remember when you are placing the cams that there is no tension on the cam chain.  Count links on the chain when you are placing the chain instead of doing it by eyeballing.  While you put the tensioner in, it might help to have someone watch the cam gears and put some tension by hand to make sure that they don't skip. 

I feel like the problem comes into play when I have to tighten down the exhaust cam, which pushes exhaust valve 1 down, when setting the comes they seem closer to the correct position, but when the exhaust cam depresses the exhaust valve it changes the positioning of the cam.

Yeah, that sounds like another challenging part.  It was a few years ago when I did mine.  I must have been lucky to get it on the first or second try.