I am going to bolt my rocker assembly to cylinder and it is not completely flush. If I push one side the other moves up. I do have cam dowel at tdc. Seems like If intrigue the head bolts down I will bend something. Thanks.

 

No matter where you have the cam positioned, some of the valves are going to be open.
This means that that those valves rockers will be standing on their cam lobes and forcing those valves springs to compress.
This is why the rocker assembly will not lay flat.
Tighten all the head bolts little by little until all the rocker towers come flat onto the head.
The force required should be minimal.
It IS important that both the cam and crank are set correctly in relationship to each other, or there is risk that open valves could interfere with an improperly positioned piston and be damaged.
Once its down flat, you can torque it down in several steps, using the correct bolt sequence.