Why is it running like crap

G'day, I finished assembling the motor on my KZ 1000 and it is running like crap. I removed the cam cover to check the cam timing and also removed the head to check for bent valves, (none found). Reasembled the head and refitted to motor. double checked the fitting of the cam shafts and I am 99.999% sure they are correct.
I wanted to check that I am reading the valve gap correctly before testing other possibilities. The book says to get the - - marks parallel to the edge of the head with one of the shafts, ( this means that I can check the valve gap on the valves either 1&3 or 2&4) which are on that shaft. Does this mean that one cam lobe is pointing to 12 o'clock and the other is pointing more or less to the edge of the head ie at 3 or 9 o'clock.
I then measure the gaps and then rotate the crankshaft one turn to do the other two valves on that shaft. I then line up the markers on the other shaft and repeat the process. Once I have confirmed that this is either right or wrong I will then start to trouble shoot other posibilities. regards Neil

My book says you check the valve gaps when the valve is pointing directly away from the lifter bucket.

The easiest way to check the valve clearances is to just rotate the engine by hand until the cam lobe is 180 degrees away from whatever valve your checking.

The picture you posted, showing the cams and the head together on the right/ #4 side is showing cams in time, if the 1-4 "T" mark is lined up. Great picture. I saved it so I can post it the next time there is another "Cam Timing" Thread. This clearly shows the lobe position, and the Notches on the ends of the cams, in relation to the gasket surface.
I'd check those valve clearances, then compression. Remember to hold the throttle open when testing compression.
Could be you have Carb, or Ignition issues. Still running points and condensers? If so whats the condition there, and have you checked the ignition timing? The mechanical advancer, have you ever serviced it so it moves freely, snaps back against the spring tension?
If you have it running, you could do a video and post a link to it here for everyone to watch/ post opinions.