Joe C. will have used your specs to select a needle profile for the carbs. Once those needles were installed he would set the "basic" starting adjustments for the carbs. Balancing the airflow and fine tuning of the mixture cannot be done until your engine is running. Be sure to read over the carb adjustment process in as many sources as you have access to in print and online. Wrap your head around the process and what each adjustment is for and you will be OK.
You are correct, you should check the specs for your cam regarding the rocker clearance. When discussing timing, particularly when an engine rebuild is involved, it is helpful to include keywords "ignition" and "valve" where appropriate. You will have to have set your valve timing correctly during the engine build. That's the part that involves proper orientation of the timing pulleys and chain. The static ignition timing needs to be set by eye or test lamp to get the engine to start. Once at temperature you can set the dynamic timing with a light.
When you are fitting the plugs, cap, and rotor, remember that the distributor rotor turns COUNTERCLOCKWISE. Therefore, your firing order will be 1-3-4-2 counterclockwise around the distributor cap with plug number 1 being at the water pump end of the engine.