My cams were not flush square with the head or each other either, but I rotated them individually until they were. I just used a crescent wrench on the square to rotate the cam while it was unbolted from the gear- I did this for both cams. I'm not sure if that is a good way to go about correcting the alignment but it worked great for me. I used a ruler to check for square.

My cams were only a little bit off to begin with though. It sounds to me if you don't have interference from cranking it over by hand that you won't have it with the engine running. But one or both of your cams may be advanced/retarded?
Thanks for the reply all. I've changed the oil, filter and refilled the coolant. I need to route the and installed spark plugs and torque down the VC. will probably be cranking it over today. fingers crossed. BTW JP, my cam angles looked just like yours in the photo.