Yes, make the left and right as close as your reasonably can so that when you go to synch the carbs afterwards, you'll *know* that the (2) cylinders are sucking in air/fuel at the same rate, so any imbalance will be in the carb adjustments.
0.004" intake and 0.008" exhaust work fine - I think I run mine at about .005"-.006" intake and 0.008 exhaust. You don't really want to go more than this or the valves do get a bit extra "clackety-clackety". Though, as we say in Airhead land - "Happy valves are tappy valves!". When you cannot hear any valvetrain noise, that is when you have to start to worry and get in there